April 28, 2020

Bioconductors:

We are pleased to announce Bioconductor 3.11, consisting of 1903 software packages, 391 experiment data packages, 961 annotation packages, and 27 workflows.

There are 98 new software packages, 10 new data experiment packages, 5 new annotation packages, 1 new workflow, and many updates and improvements to existing packages; Bioconductor 3.11 is compatible with R 4.0.0, and is supported on Linux, 32- and 64-bit Windows, and macOS 10.13 High Sierra or higher. This release will include an updated Bioconductor Amazon Machine Image and Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

• Getting Started with Bioconductor 3.11
• New Software Packages
• New Data Experiment Packages
• New Annotation Packages
• New Workflow
• NEWS from new and existing software packages
• NEWS from new and existing data experiment packages
• NEWS from new and existing workflows
• Deprecated and Defunct Packages

Getting Started with Bioconductor 3.11

To update to or install Bioconductor 3.11:

1. Install R 4.0.0. Bioconductor 3.11 has been designed expressly for this version of R.

2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 98 new software packages in this release of Bioconductor.

• basilisk Installs a self-contained Python instance that is managed by the R installation. This aims to provide a consistent Python version that can be used reliably by Bioconductor packages. Module versions are also controlled to guarantee consistent behavior on different user systems.

• basilisk.utils Implements utilities for installation of the basilisk package, primarily to avoid re-writing the same R code in both the configure script (for centrally administered R installations) and in the lazy installation mechanism (for distributed binaries). It is highly unlikely that developers - or, heaven forbid, end-users! - will need to interact with this package directly; they should be using the basilisk package instead.

• BgeeCall Reference intergenic regions are generated by the Bgee RNA-Seq pipeline. These intergenic regions are used to generate all Bgee RNA-Seq present/absent expression calls. BgeeCall now allows to generate present/absent calls for any RNA-Seq library as long as reference intergenic sequences have been generated for the corresponding species. The threshold of present/absent expression is no longer arbitrary defined but is calculated based on expression of all RNA-Seq libraries integrated in Bgee.

• biobtreeR The biobtreeR package provides an interface to biobtree tool which covers large set of bioinformatics datasets and allows search and chain mappings functionalities.

• BiocDockerManager Package works analogous to BiocManager but for docker images. Use the BiocDockerManager package to install and manage docker images provided by the Bioconductor project. A convenient package to install images, update images and find which Bioconductor based docker images are available.

• BRGenomics This package provides useful and efficient utilites for the analysis of high-resolution genomic data using standard Bioconductor methods and classes. BRGenomics is feature-rich and simplifies a number of post-alignment processing steps and data handling. Emphasis is on efficient analysis of multiple datasets, with support for normalization and blacklisting. Included are functions for: spike-in normalizing data; generating basepair-resolution readcounts and coverage data (e.g. for heatmaps); importing and processing bam files (e.g. for conversion to bigWig files); generating metaplots/metaprofiles (bootstrapped mean profiles) with confidence intervals; conveniently calling DESeq2 without using sample-blind estimates of genewise dispersion; among other features.

• CARNIVAL An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs’ weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

• ceRNAnetsim This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.

• CeTF This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al. 2010) algorithm. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network and can be applied to any correlation-based network including but not limited to gene co-expression networks, while the RIF algorithm identify critical Transcription Factors (TF) from gene expression data. These two algorithms when combined provide a very relevant layer of information for gene expression studies (Microarray, RNA-seq and single-cell RNA-seq data).

• CiteFuse CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.

• clustifyr Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.

• cmapR The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common (CMap) data objects, such as annotated matrices and collections of gene sets.

• combi Combine quasi-likelihood estimation, compositional regression models and latent variable models for integrative visualization of several omics datasets. Both unconstrained and constrained integration is available, the results are shown as interpretable multiplots.

• CoreGx A collection of functions and classes which serve as the foundation for our lab’s suite of R packages, such as ‘PharmacoGx’ and ‘RadioGx’. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future ‘Gx’ suite programs. Major features include a ‘CoreSet’ class, from which ‘RadioSet’ and ‘PharmaSet’ are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.

• CSSQ This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.

• ctgGEM Cell Tree Generator for Gene Expression Matrices (ctgGEM) streamlines the building of cell-state hierarchies from single-cell gene expression data across multiple existing tools for improved comparability and reproducibility. It supports pseudotemporal ordering algorithms and visualization tools from monocle, cellTree, TSCAN, sincell, and destiny, and provides a unified output format for integration with downstream data analysis workflows and Cytoscape.

• cytomapper Highly multiplexed imaging cytometry acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualized across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualized on segmented cell areas. This package contains functions for the visualization of multiplexed read-outs and cell-level information obtained by multiplexed imaging cytometry. The main functions of this package allow 1. the visualization of pixel-level information across multiple channels and 2. the display of cell-level information (expression and/or metadata) on segmentation masks.

• DAMEfinder ‘DAMEfinder’ offers functionality for taking methtuple or bismark outputs to calculate ASM scores and compute DAMEs. It also offers nice visualization of methyl-circle plots.

• dearseq Differential Expression Analysis RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights. Perform both gene-wise and gene set analyses, and can deal with repeated or longitudinal data. Methods are detailed in: Agniel D & Hejblum BP (2017) Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604. and Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2019). dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, bioRxiv 635714.

• DIAlignR To obtain unbiased proteome coverage from a biological sample, mass-spectrometer is operated in Data Independent Acquisition (DIA) mode. Alignment of these DIA runs establishes consistency and less missing values in complete data-matrix. This package implements dynamic programming with affine gap penalty based approach for pair-wise alignment of analytes. A hybrid approach of global alignment (through MS2 features) and local alignment (with MS2 chromatograms) is implemented in this tool.

• distinct distinct is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via hierarchical non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. While most methods for differential expression target differences in the mean abundance between conditions, distinct, by comparing full cdfs, identifies, both, differential patterns involving changes in the mean, as well as more subtle variations that do not involve the mean (e.g., unimodal vs. bi-modal distributions with the same mean). distinct is a general and flexible tool: due to its fully non-parametric nature, which makes no assumptions on how the data was generated, it can be applied to a variety of datasets. It is particularly suitable to perform differential state analyses on single cell data (i.e., differential analyses within sub-populations of cells), such as single cell RNA sequencing (scRNA-seq) and high-dimensional flow or mass cytometry (HDCyto) data. To use distinct one needs data from two or more groups of samples (i.e., experimental conditions), with at least 2 samples (i.e., biological replicates) per group.

• dittoSeq A universal, user friendly, single-cell and bulk RNA sequencing visualization toolkit that allows highly customizable creation of color blindness friendly, publication-quality figures. dittoSeq accepts both SingleCellExperiment (SCE) and Seurat objects, as well as the import and usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data. Visualizations include dimensionality reduction plots, heatmaps, scatterplots, percent composition or expression across groups, and more. Customizations range from size and title adjustments to automatic generation of annotations for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton plot, hidden data overlay upon cursor hovering via ggplotly conversion, and many more. All with simple, discrete inputs. Color blindness friendliness is powered by legend adjustments (enlarged keys), and by allowing the use of shapes or letter-overlay in addition to the carefully selected dittoColors().

• dpeak dPeak is a statistical framework for the high resolution identification of protein-DNA interaction sites using PET and SET ChIP-Seq and ChIP-exo data. It provides computationally efficient and user friendly interface to process ChIP-seq and ChIP-exo data, implement exploratory analysis, fit dPeak model, and export list of predicted binding sites for downstream analysis.

• Dune Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability.

• easyreporting An S4 class for facilitating the automated creation of rmarkdown files inside other packages/software, even without knowing rmarkdown language. Best if implemented in functions as “recursive” style programming.

• eisaR Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.

• EnMCB Creation of the correlated blocks using DNA methylation profiles. A stacked ensemble of machine learning models, which combined the support vector machine and elastic-net regression model, can be constructed to predict disease progression.

• EpiTxDb EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA to be modified and the literature references each modification is associated with.

• exomePeak2 exomePeak2 provides bias awared quantification and peak detection on Methylated RNA immunoprecipitation sequencing data (MeRIP-Seq). MeRIP-Seq is a commonly applied sequencing technology to measure the transcriptome-wide location and abundance of RNA modification sites under a given cellular condition. However, the quantification and peak calling in MeRIP-Seq are sensitive to PCR amplification bias which is prevalent in next generation sequencing (NGS) techniques. In addition, the RNA-Seq based count data exhibits biological variation in small reads count. exomePeak2 collectively address these challanges by introducing a rich set of robust data science models tailored for MeRIP-Seq. With exomePeak2, users can perform peak calling, modification site quantification, and differential analysis with a straightforward one-step function. Alternatively, users could define personalized methods for their own analysis through multi-step functions and diagnostic plots.

• ExploreModelMatrix Given a sample data table and a design formula, generate an interactive application to explore the resulting design matrix.

• FRASER Detection of rare aberrant splicing events in transcriptome profiles. The workflow aims to assist the diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

• frenchFISH FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.

• GCSConnection Create R ‘connection’ objects to google cloud storage buckets using the Google REST interface. Both read and write connections are supported. The package also provide functions to view and manage files on Google Cloud.

• GeneTonic This package provides a Shiny application that aims to combine at different levels the existing pieces of the transcriptome data and results, in a way that makes it easier to generate insightful observations and hypothesis - combining the benefits of interactivity and reproducibility, e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist.

• GGPA Genome-wide association studies (GWAS) is a widely used tool for identification of genetic variants associated with phenotypes and diseases, though complex diseases featuring many genetic variants with small effects present difficulties for traditional these studies. By leveraging pleiotropy, the statistical power of a single GWAS can be increased. This package provides functions for fitting graph-GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy. ‘GGPA’ package provides user-friendly interface to fit graph-GPA models, implement association mapping, and generate a phenotype graph.

• glmGamPoi Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.

• gmoviz Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. gmoviz provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.

• GPA This package provides functions for fitting GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy information and annotation data. In addition, it also includes ShinyGPA, an interactive visualization toolkit to investigate pleiotropic architecture.

• HIPPO For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.

• iSEEu iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.

• LACE LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.

• MatrixGenerics S4 generic functions modeled after the ‘matrixStats’ API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.

• MEAT This package estimates epigenetic age in skeletal muscle, using DNA methylation data generated with Illumina Infinium technology (HM27, HM450 and HMEPIC).

• metaseqR2 Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

• methylSig MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.

• MicrobiotaProcess MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It supports calculating alpha index and provides functions to visualize rarefaction curves. Moreover, it also supports visualizing the abundance of taxonomy of samples. And It also provides functions to perform the PCA, PCoA and hierarchical cluster analysis. In addition, MicrobiotaProcess also provides a method for the biomarker discovery of metagenome or other datasets.

• mitch mitch is an R package for multi-contrast enrichment analysis. At it’s heart, it uses a rank-MANOVA based statistical approach to detect sets of genes that exhibit enrichment in the multidimensional space as compared to the background. The rank-MANOVA concept dates to work by Cox and Mann (https://doi.org/10.1186/1471-2105-13-S16-S12). mitch is useful for pathway analysis of profiling studies with one, two or more contrasts, or in studies with multiple omics profiling, for example proteomic, transcriptomic, epigenomic analysis of the same samples. mitch is perfectly suited for pathway level differential analysis of scRNA-seq data. The main strengths of mitch are that it can import datasets easily from many upstream tools and has advanced plotting features to visualise these enrichments.

• MOMA This package implements the inference of candidate master regulator proteins from multi-omics’ data (MOMA) algorithm, as well as ancillary analysis and visualization functions.

• MsCoreUtils MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning), quantitative aggregation functions (median polish, robust summarisation, …), missing data imputation, data normalisation (quantiles, vsn, …) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

• netboxr NetBox is a software tool for performing network analysis on human interaction networks. It is pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.

• netDx netDx is a general-purpose algorithm to build a patient classifier from heterogenous patient data. The method converts data into patient similarity networks at the level of features. Feature selection identifies features of predictive value to each class. Methods are provided for versatile predictor design and performance evaluation using standard measures. netDx natively groups molecular data into pathway-level features and connects with Cytoscape for network visualization of pathway themes. For method details see: Pai et al. (2019). netDx: interpretable patient classification using integrated patient similarity networks. Molecular Systems Biology. 15, e8497

• NoRCE While some non-coding RNAs (ncRNAs) have been found to play critical regulatory roles in biological processes, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs set needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together, and this spatial proximity hints at a functional association. Based on this idea, we present an R package, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out by using the functional annotations of the coding genes located proximally to the input ncRNAs. NoRCE allows incorporating other biological information such as the topologically associating domain (TAD) regions, co-expression patterns, and miRNA target information. NoRCE repository includes several data files, such as cell line specific TAD regions, functional gene sets, and cancer expression data. Additionally, users can input custom data files. Results can be retrieved in a tabular format or viewed as graphs. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm and yeast.

• NPARC Perform non-parametric analysis of response curves as described by Childs, Bach, Franken et al. (2019): Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.

• OpenStats Package contains several methods for statistical analysis of genotype to phenotype association in high-throughput screening pipelines.

• optimalFlow Optimal-transport techniques applied to supervised flow cytometry gating.

• packFinder Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).

• peco Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently, allows to identify cyclic trend of gene expression levels along the cell cycle. This package provides method and training data, which includes scRNA-seq data collected from 6 individual cell lines of induced pluripotent stem cells (iPSCs), and also continuous cell cycle phase derived from FUCCI fluorescence imaging data.

• PloGO2 Functions for enrichment analysis and plotting gene ontology or KEGG pathway information for multiple data subsets at the same time. It also enables encorporating multiple conditions and abundance data.

• pmp Methods and tools for (pre-)processing of metabolomics datasets (i.e. peak matrices), including filtering, normalisation, missing value imputation, scaling, and signal drift and batch effect correction methods. Filtering methods are based on: the fraction of missing values (across samples or features); Relative Standard Deviation (RSD) calculated from the Quality Control (QC) samples; the blank samples. Normalisation methods include Probabilistic Quotient Normalisation (PQN) and normalisation to total signal intensity. A unified user interface for several commonly used missing value imputation algorithms is also provided. Supported methods are: k-nearest neighbours (knn), random forests (rf), Bayesian PCA missing value estimator (bpca), mean or median value of the given feature and a constant small value. The generalised logarithm (glog) transformation algorithm is available to stabilise the variance across low and high intensity mass spectral features. Finally, this package provides an implementation of the Quality Control-Robust Spline Correction (QCRSC) algorithm for signal drift and batch effect correction of mass spectrometry-based datasets.

• PubScore Calculates the importance score for a given gene. The importance score is the total counts of articles in the pubmed database that are a result for that gene AND each term of a list.

• randRotation A collection of methods for performing random orthogonal transformations (random rotations) on high-dimensional data (e.g. microarray or RNA-seq data) with batch structure. The random rotation approach allows exact testing of dependent test statistics with linear models following arbitrary, particularly non-linear, batch effect correction methods. The package further provides methods for estimating the local degrees of freedom of data mappings.

• receptLoss receptLoss identifies genes whose expression is lost in subsets of tumors relative to normal tissue. It is particularly well-suited in cases where the number of normal tissue samples is small, as the distribution of gene expression in normal tissue samples is approximated by a Gaussian. Originally designed for identifying nuclear hormone receptor expression loss but can be applied transcriptome wide as well.

• reconsi Improves simultaneous inference under dependence of tests by estimating a collapsed null distribution through resampling. Accounting for the dependence between tests increases the power while reducing the variability of the false discovery proportion. This dependence is common in genomics applications, e.g. when combining flow cytometry measurements with microbiome sequence counts.

• regutools RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.

• rfaRm rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.

• rhdf5filters Provides a collection of compression filters for use with HDF5 datasets.

• ribor The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents.

• ribosomeProfilingQC Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

• RNAAgeCalc It has been shown that both DNA methylation and RNA transcription are linked to chronological age and age related diseases. Several estimators have been developed to predict human aging from DNA level and RNA level. Most of the human transcriptional age predictor are based on microarray data and limited to only a few tissues. To date, transcriptional studies on aging using RNASeq data from different human tissues is limited. The aim of this package is to provide a tool for across-tissue and tissue-specific transcriptional age calculation based on GTEx RNASeq data.

• ROCpAI The package analyzes the Curve ROC, identificates it among different types of Curve ROC and calculates the area under de curve through the method that is most accuracy. This package is able to standarizate proper and improper pAUC.

• ROSeq A rank based approach to modeling gene expression with filtered and normalized read count matrix. Takes in the complete filtered and normalized read count matrix, the location of the two sub-populations and the number of cores to be used.

• rrvgo Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.

• rSWeeP The SWeeP method was developed to favor the analizes between amino acids sequences and to assist alignment free phylogenetic studies. This method is based on the concept of sparse words, which is applied in the scan of biological sequences and its the conversion in a matrix of ocurrences. Aiming the generation of low dimensional matrices of Amino Acid Sequence occurrences.

• sarks Suffix Array Kernel Smoothing (see https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797), or SArKS, identifies sequence motifs whose presence correlates with numeric scores (such as differential expression statistics) assigned to the sequences (such as gene promoters). SArKS smooths over sequence similarity, quantified by location within a suffix array based on the full set of input sequences. A second round of smoothing over spatial proximity within sequences reveals multi-motif domains. Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.

• scClassify scClassify is a multiscale classification framework for single-cell RNA-seq data based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references.

• scHOT Single cell Higher Order Testing (scHOT) is an R package that facilitates testing changes in higher order structure of gene expression along either a developmental trajectory or across space. scHOT is general and modular in nature, can be run in multiple data contexts such as along a continuous trajectory, between discrete groups, and over spatial orientations; as well as accommodate any higher order measurement such as variability or correlation. scHOT meaningfully adds to first order effect testing, such as differential expression, and provides a framework for interrogating higher order interactions from single cell data.

• scMAGeCK scMAGeCK is a computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data (CROP-seq)

• SCOPE Whole genome single-cell DNA sequencing (scDNA-seq) enables characterization of copy number profiles at the cellular level. This circumvents the averaging effects associated with bulk-tissue sequencing and has increased resolution yet decreased ambiguity in deconvolving cancer subclones and elucidating cancer evolutionary history. ScDNA-seq data is, however, sparse, noisy, and highly variable even within a homogeneous cell population, due to the biases and artifacts that are introduced during the library preparation and sequencing procedure. Here, we propose SCOPE, a normalization and copy number estimation method for scDNA-seq data. The distinguishing features of SCOPE include: (i) utilization of cell-specific Gini coefficients for quality controls and for identification of normal/diploid cells, which are further used as negative control samples in a Poisson latent factor model for normalization; (ii) modeling of GC content bias using an expectation-maximization algorithm embedded in the Poisson generalized linear models, which accounts for the different copy number states along the genome; (iii) a cross-sample iterative segmentation procedure to identify breakpoints that are shared across cells from the same genetic background.

• scry Many modern biological datasets consist of small counts that are not well fit by standard linear-Gaussian methods such as principal component analysis. This package provides implementations of count-based feature selection and dimension reduction algorithms. These methods can be used to facilitate unsupervised analysis of any high-dimensional data such as single-cell RNA-seq.

• scTHI scTHI is an R package to identify active pairs of ligand-receptors from single cells in order to study,among others, tumor-host interactions. scTHI contains a set of signatures to classify cells from the tumor microenvironment.

• selectKSigs A package to suggest the number of mutational signatures in a collection of somatic mutations using calculating the cross-validated perplexity score.

• SimFFPE This package simulates artifact chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissue.

• SingleCellSignalR Allows single cell RNA seq data analysis, clustering, creates internal network and infers cell-cell interactions.

• snapcount snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in).

• sparseMatrixStats High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.

• spicyR spicyR provides a series of functions to aid in the analysis of both immunofluorescence and mass cytometry imaging data as well as other assays that can deeply phenotype individual cells and their spatial location.

• spqn The spqn package implements spatial quantile normalization (SpQN). This method was developed to remove a mean-correlation relationship in correlation matrices built from gene expression data. It can serve as pre-processing step prior to a co-expression analysis.

• struct Defines and includes a set of class-based templates for developing and implementing data processing and analysis workflows, with a strong emphasis on statistics and machine learning. The templates can be used and where needed extended to ‘wrap’ tools and methods from other packages into a common standardised structure to allow for effective and fast integration. Model objects can be combined into sequences, and sequences nested in iterators using overloaded operators to simplify and improve readability of the code. STATistics Ontology (STATO) has been integrated and implemented to provide standardised definitions for methods, inputs and outputs wrapped using the class-based templates.

• structToolbox An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics, with a strong emphasis on statistics and machine learning. This toolbox allows the user to build extensive and standardised workflows for data analysis. The methods and tools have been implemented using class-based templates provided by the struct (Statistics in R Using Class-based Templates) package. The toolbox includes pre-processing methods (e.g. signal drift and batch correction, normalisation, missing value imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and PLS, including cross-validation and permutation testing) as well as machine learning methods (e.g. Support Vector Machines). The STATistics Ontology (STATO) has been integrated and implemented to provide standardised definitions for the different methods, inputs and outputs.

• SynExtend Shared order between genomic sequences provide a great deal of information. Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. SynExtend provides tools for extracting information from Synteny objects.

• TAPseq Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.

• TBSignatureProfiler Signatures of TB progression, TB disease, and other TB disease states have been created. This package makes it easy to profile RNA-Seq data using these signatures and common signature profiling tools including ASSIGN, GSVA, and ssGSEA.

• tidybulk This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.

• timeOmics timeOmics is a generic data-driven framework to integrate multi-Omics longitudinal data measured on the same biological samples and select key temporal features with strong associations within the same sample group. The main steps of timeOmics are: 1. Plaform and time-specific normalization and filtering steps; 2. Modelling each biological into one time expression profile; 3. Clustering features with the same expression profile over time; 4. Post-hoc validation step.

• TreeAndLeaf TreeAndLeaf package comes as an alternative to solve problems regarding dendrogram plotting, such as the lack of space when the dendrogram is too large and the need for adding more layers of information. It treats a whole dendrogram as a tree, in which the observations are represented by the leaves.

• tscR Clustering for time series data using slope distance and/or shape distance.

• vasp Discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures.

• weitrix Data type and tools for working with matrices having precision weights and missing data. This package provides a common representation and tools that can be used with many types of high-throughput data. The meaning of the weights is compatible with usage in the base R function “lm” and the package “limma”. Calibrate weights by scaling weights row-wise to account for known predictors of precision. Find PCA-like components of variation even with many missing values, rotated so that individual components may be meaningfully interpreted. DelayedArray matrices and BiocParallel are supported.

New Data Experiment Packages

There are 10 new data experiment packages in this release of Bioconductor.

• curatedAdipoArray A curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.

• dorothea This package contains human and mouse TF regulons. The human regulons were curated and collected from different types of evidence such as literature curated resources, ChIP-seq peaks, TF binding site motifs and interactions inferred directly from gene expression. The mouse regulons were constructed by mapping the human gene symbols to their orthologs in mice. Those regulons can be coupled with any statistical method that aims to analyse gene sets to infer TF activity from gene expression data. Preferably the statistical method viper is used.

• gpaExample Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS).

• HighlyReplicatedRNASeq Gene-level count matrix data for bulk RNA-seq dataset with many replicates. The data are provided as easy to use SummarizedExperiment objects. The source data that is made accessible through this package comes from https://github.com/bartongroup/profDGE48.

• optimalFlowData Data files used as examples and for testing of the software provided in the optimalFlow package.

• scTHI.data Data for the vignette and tutorial of the package scTHI.

• SingleCellMultiModal SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. The current focus is on datasets that use new technologies such as scNMT and scM&T.

• spatialLIBD Inspect interactively the spatial transcriptomics 10x Genomics Visium data from Maynard, Collado-Torres et al, 2020 analyzed by Lieber Institute for Brain Development researchers and collaborators.

• spqnData Bulk RNA-seq from GTEx on 4,000 randomly selected, expressed genes. Data has been processed for co-expression analysis.

• WGSmapp This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin. “Blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included. The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X for illustration purposes.

New Annotation Packages

There are 5 new annotation packages in this release of Bioconductor.

• EpiTxDb.Hs.hg38
• EpiTxDb.Sc.sacCer3
• EpiTxDb.Mm.mm10
• MafH5.gnomAD.r3.0.GRCh38_3.11.0
• phastCons30way.UCSC.hg38_3.11.1

New Workflow Packages

There is 1 new workflow package in this release of Bioconductor.

• fluentGenomics An extended workflow using the plyranges and tximeta packages for fluent genomic data analysis. Use tximeta to correctly import RNA-seq transcript quantifications and summarize them to gene counts for downstream analysis. Use plyranges for clearly expressing operations over genomic coordinates and to combine results from differential expression and differential accessibility analyses.

NEWS from new and existing Software Packages

ACE

             Changes in version 1.5.2 (2020-04-14)                  

• updated maintainer e-mail address

             Changes in version 1.5.1 (2020-01-14)                  
  

• fixed a bug in getadjustedsegments that joined adjacent chromosomes with same segment values

affylmGUI

                   Changes in version 1.62.0                        

• Update affylmGUI to use AnnotationDbi and the new “.db” style probe-set annotation packages.

• Reduce overlap with the limma package. affylmGUI now uses the limma functions lmFit(), eBayes(), topTable() and limmaUsersGuide() directly.

• Remove functions ALGchangeLog(), ALGlimmaUsersGuide(), deleteItemFromList(), toptable2() and topTable2().

• Add affylmGUI-package help file. Split existing help file into two.

• Various internal code updates and simplifications.

alevinQC

                    Changes in version 1.3.1                        

• Added the possibility of providing custom cell barcode sets

AlphaBeta

             Changes in version 1.2.1 (2020-04-20)                  

• Fixed bugs.

• Made the following significant changes + Using ape package to make tree. + Added some plots.

• Added SOMA functions.

• Plotting estimates

alsace

                   Changes in version 1.22.1                        

• replaced two calls to ‘class’ to ‘inherits’

AneuFinder

                   Changes in version 1.15.2                        

BUG FIXES

• Compatibility update: Replaced deprecated fetchExtendedChromInfoFromUCSC() with getChromInfoFromUCSC().

AnnotationHub

                   Changes in version 2.19.0                        

BUG FIX

• (2.19.12) change has_internet to nslookup to avoid locations that do not have access to google dns.

NEW FEATURES

• (2.19.8) Fixed messages to be more informative

• (2.19.8) trycatch around bfcneedsupdate/bfcdownload for sqlite database to prevent error when internet is spotty and databse source cannot be checked for a newer version.

• (2.19.4) trycatch around bfcneedsupdate call will prevent error when internet is spotty and resource cannot be checked for a newer version.

• (2.19.3) New function removeResources for removing locally downloaded cached resources. Nicer interface than using cache. Improved documentation on use of setting a cache to NULL to also remove resources.

• (2.19.2) Adds option ask to constructor. Default: True. Ask will ask user to create default AnnotationHub location and if in an non interactive session utilize a temporary directory. If False, the default directory is created and utilized without prompting.

USER-VISIBLE MODIFICATIONS

• (2.19.1) Improve ERROR message when resource isn’t found. Also involved updating RecordStatus function. If resource hasn’t been completely removed from database, gives when the resource was removed. If the resource is available but after the snapshot date being utilized, specialized message.

AnnotationHubData

                   Changes in version 1.17.0                        

MODIFICATIONS

• 1.17.3 add check for valid Title and Description in metadata file. It should not be empty or NA

• 1.17.2 add XML as valid source type

• 1.17.1 add GSEMatrix as valid source type

anota2seq

                    Changes in version 1.9.1                        

• Fixed coding that would results in errors in R version 4.0 related to used of class(…) == “x”.

APAlyzer

             Changes in version 1.1.2 (2020-03-18)                  

• Add the download_testbam to download the testing data bam files.

• Add extra section ‘Complete Analysis Example’ in vignettes

• Revise some typos in vignettes and mans.

             Changes in version 1.1.1 (2020-03-15)                  
  

• Add the PAS2GEF to convert GTF to PAS reference.

• Add the REF4PAS to generate reference region for both 3’UTR and introic PAS at the same time.

• Add the APAVolcano and APABox to plot the APAdiff results.

• Add Adjusted p-value option in APAdiff

• Allow the user to set argument minMQS to filter minimum mapping quality score of counted reads.

• Add the build-in PAS reference for hg38 and mm10.

• Add the build-in PAS reference for all PASs including conserved and non-conserved.

• Update vignettes and mans.

• PAS reference regions are now moved to a separate repo.

             Changes in version 1.1.0 (2020-02-27)                  
  

• Revise some typos in vignettes and mans.

             Changes in version 1.0.1 (2020-01-28)                  
  

• Revise some typos in vignettes and mans.

aroma.light

             Changes in version 3.17.1 (2019-12-09)                 

CODE REFACTORING

• Now importing throw() from R.oo instead of R.methodsS3.

             Changes in version 3.17.0 (2019-10-30)                 
  

• The version number was bumped for the Bioconductor devel version, which is now BioC 3.11 for R (>= 3.6.1).

artMS

                    Changes in version 1.6.0                        

• Major package updates. It addresses most of the warnings and messages from required packages

• Analysis of Protein Acetylation now supported.

• General to all Quality control plots: update default names for all pdf outputs

• QC artmsQualityControlEvidenceExtended():

  • New plots: peptide and protein overlap across bioreplicates and conditions (plotPEPTOVERLAP and plotPROTOVERLAP)
  • Updates and improves all the plots, affecting font size and other aesthetic options
  • Change parameter “plotIC” to “plotPCA” in artmsQualityControlEvidenceExtended()

• QC artmsQualityControlEvidenceBasic():

  • Depracated: Plot correlation distributions
  • Updated and improved all the plots, affecting font size and other aesthetic

• More data testing datasets available:

  • artms_data_ph_contrast: contrast object for available the PH example dataset
  • artms_data_ph_config: configuration yaml object for the available PH example dataset
  • artms_data_ph_msstats_results: results data object from running artmsQuantification
  • artms_data_ph_msstats_modelqc: modelqc data object from running artmsQuantification

• Vignette updated

• Other minor fixes / improvements

             Changes in version 1.4.3 (2020-02-08)                  
  

• artmsAnalysisQuantifications(), several updates:

  • change default value for “l2fc_thres” to 1
  • change defult value for “output_dir” to “analysis_quant”
  • NEW option: “outliers”. It allows to remove outliers from abundance data

• Fix bug affecting artmsQualityControlSummaryExtended()

             Changes in version 1.4.2 (2019-12-06)                  
  

• Fixed a crash when impute fails due to missing outlier data (part 2)

             Changes in version 1.4.1 (2019-12-06)                  
  

• Fixed a crash when impute fails due to missing outlier data

ASpediaFI

             Changes in version 1.1.4 (2020-04-01)                  

• Changed formats of outputs from ASpediaFI

             Changes in version 1.1.3 (2020-03-27)                  
  

• Changed maintainer’s email address

             Changes in version 1.1.2 (2020-03-04)                  
  

• Modified to ensure that permutation is performed only on gene nodes.

             Changes in version 1.1.1 (2019-12-12)                  
  

• Added permutation test to DRaWR

ASSIGN

             Changes in version 1.23.1 (2020-04-18)                 

• ASSIGN no longer changes the working directory

• ASSIGN requires that output files do not exist before functions run

ATACseqQC

                   Changes in version 1.11.9                        

• Fix a issue for splitGAlignmentsList, splitGAlignments by supply the header info to mergeBam.

                   Changes in version 1.11.8                        
  

• Fix a issue ‘mergeBam’ ‘destination’ exists, ‘overwrite’ is FALSE for splitGAlignmentsByCut.

                   Changes in version 1.11.7                        
  

• fix a typo in doc for readBamFile.

                   Changes in version 1.11.6                        
  

• fix the sample for shiftGAlignments.

                   Changes in version 1.11.5                        
  

• add function shiftGAlignments for single end reads.

                   Changes in version 1.11.4                        
  

• Fix the issue of if there is no reads in bam file for shiftGAlignmentsList.

                   Changes in version 1.11.2                        
  

• Fix the issue of “[E::sam_parse1] unrecognized type N”.

                   Changes in version 1.11.1                        
  

• Add flag parameter for splitBam.

Autotuner

                    Changes in version 1.1.2                        

• Updated ploting function of DKE to make it easier to evaluate the results. o Added a new xlim filter to DKE ploting function o Added some flags to check for file types while using AutoTuner

             Changes in version 1.0.1 (2019-07-06)                  
  

• Added DOI to cite code through zenodo.

BANDITS

                    Changes in version 1.3.4                        

• R.utils added to Imports (needed to load gzipped equivalence classes from Salmon v. 1.2.0 onwards)

                    Changes in version 1.3.3                        
  

• citation updated

                    Changes in version 1.3.2                        
  

• added a new constraint: min 5 counts per group are required to analyze a group

                    Changes in version 1.3.1                        
  

• bug fixed in ‘test_DTU’ function (giving error: “object ‘n_genes’ not found”)

• Added 1 section of the vignette for inference with 3 groups

                    Changes in version 1.2.2                        
  

• citation updated

                    Changes in version 1.2.1                        
  

• fixed bugs and incorporated edits up to version 1.3.2

BASiCS

             Changes in version 2.0.0 (2020-04-01)                  

• Improve UI for BASiCS_TestDE BASiCS_TestHVG/BASiCS_TestLVG and related functions by creating classes. Usage of objects documented in vignette.

• Reduce code duplication and refactor plots to use ggplot2.

• Add rudimentary unit tests for loading and some class methods. Fix several minor bugs.

• Change barplot in variance decomposition function to use ggplot2.

             Changes in version 1.99.1 (2020-04-14)                 
  

• Minor change in documentation of BASiCS_VarianceDecomp to use ggplot2 as reference linl (instead of RColorBrewer) link to

             Changes in version 1.99.0 (2020-04-07)                 
  

• Minor changes in vignette to increase figure sizes

• Version number updated to follow Bioc guidelines

             Changes in version 1.9.26 (2020-03-25)                 
  

• Bugfix in BASiCS_Sim

             Changes in version 1.9.25 (2020-03-13)                 
  

• ConstrainType deprecated within BASiCS_MCMC (internal option only)

• In tests_mcmc_arguments.R, adds set.seed to avoid random failure of makeExampleBASiCS_Data

             Changes in version 1.9.24 (2020-03-13)                 
  

• Removes R from Depends in DESCRIPTION.

• Minor fix in the documentation of BASiCS_PriorParam to pass BiocCheck.

             Changes in version 1.9.23 (2020-03-10)                 
  

• Adds BASiCS_PriorParam function. This function makes it easier to alter parameters for the prior distributions used in BASiCS. See issue #154.

• Adds RBFMinMax argument to BASiCS_PriorParam, which controls whether RBF are set at the minimum and maximum starting mu values.

• Adds MinGenesPerRBF argument to BASiCS_PriorParam. This controls the minimum number of genes between around the centre of each RBF.

             Changes in version 1.9.22 (2020-03-09)                 
  

• Bugfix in plot method when Param=”sigma2”

             Changes in version 1.9.21 (2020-03-05)                 
  

• Minor fix in BASiCS_MCMC to fix warning (definition of PriorMu)

             Changes in version 1.9.20 (2020-02-16)                 
  

• Fix bug in handling of tail probability tests that meant probabilities were not calculated correctly when Epsilon* = 0.

             Changes in version 1.9.19 (2020-02-16)                 
  

• Adds a while loop in BASiCS_Sim to ensure it doesn’t fail if some generated cells have zero counts.

             Changes in version 1.9.18 (2020-02-16)                 
  

• Merges empirical Bayes changes with those from divide-and-conquer

• Minor changes in unit tests to account for empirical Bayes prior ( taking ParamPrior$mu.mu as a vector, rather than a scalar)

             Changes in version 1.9.17 (2020-02-16)                 
  

• Implementation of empirical Bayes (EB) approach for mu in BASiCS_MCMC

• Additional parameter PriorMu incorporated to BASiCS_MCMC. This enables internal calculation of the EB prior.

• Creates .EmpiricalBayesMu to derive EB prior for mu.

• HiddenBASiCS_MCMC_InputCheck, HiddenBASiCS_MCMC_GlobalParams and HiddenBASiCS_MCMC_ExtraArgs renamed as .BASiCS_MCMC_InputCheck, .BASiCS_MCMC_GlobalParams and .BASiCS_MCMC_ExtraArgs.

• Fixes minor bug in .EmpiricalBayesMu

• Fixes EB approach for no-spikes case (regression and no regression)

• Updates documentation of BASiCS_MCMC to include PriorMu as a parameter

• Removes dependency to scater functions in .EmpiricalBayesMu.

             Changes in version 1.9.16 (2020-02-16)                 
  

• Adds extra line in test_sim.R to avoid warning in BiocCheck

             Changes in version 1.9.15 (2020-02-16)                 
  

• Use expect_equal in scran test (now all suitable tests)

• Minor change in test_differential_test_reg.R to use 3 instead of 2 decimal points. This hopefully avoids issues associated to a bug in round. For details see: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17668

             Changes in version 1.9.14 (2020-02-10)                 
  

• Changes coda::effectiveSize for a more efficient internal implementation.

• Adds CheckESS and MinESS arguments to BASiCS_TestDE to filter genes for differential expression testing based on effective sample size.

             Changes in version 1.9.13 (2020-02-05)                 
  

• Adds option for prior scaling parameters (relevant for new divide and conquer approach only; does not affect UI)

             Changes in version 1.9.12 (2020-01-17)                 
  

• Fixes bug in BASiCS_CorrectOffset for no-spikes case

             Changes in version 1.9.11 (2020-01-11)                 
  

• Add unit tests for each MCMC update.

             Changes in version 1.9.10 (2019-12-13)                 
  

• Further clean up in BASiCS_TestDE. Creates new internal functions to avoid duplicated code across different tests: .TestResults, .ShowTestResults

             Changes in version 1.9.9 (2019-12-12)                  
  

• Version bump after pull request merge

• R version requirement set to 3.6.0

• dimnames<- added for BASiCS_Chain objects

• Additional input checks for BASiCS_DenoisedCounts and BASiCS_DenoisedRates

             Changes in version 1.9.8 (2019-12-12)                  
  

• Clean-up for HiddenTailProbTestDE -> renamed as .TailProb. Similar for .ThresholdSearch, .EFDR and .EFNR

• Extra unit test for GenesSelect parameter in BASiCS_TestDE

• Removes HiddenThresholdSearchDetectHVG_LVG as no longer needed.

• Changes in BASiCS_DetectHVG and BASiCS_DetectLVG to reuse same hidden functions as in BASiCS_TestDE (extra potential changes exist)

             Changes in version 1.9.7 (2019-12-05)                  
  

• Fixes bug in mu updates (log(mu) - mu.mu, rather than log(mu - mu.mu)). This does not affect default prior, only empirical Bayes approach.

             Changes in version 1.9.6 (2019-12-04)                  
  

• Minor changes in test_misc.R to expose hidden functions

             Changes in version 1.9.5 (2019-12-04)                  
  

• Optional parameter added to all mcmc samplers to enable user-defined prior mean for log(mu).

• Requirement of R (>= 4.0.0) added as suggested by BiocCheck

             Changes in version 1.9.4 (2019-12-04)                  
  

• Example chain objects updated to satisfy identifiability constrain

• test_vardecomp.R updated accordingly

             Changes in version 1.9.3 (2019-12-04)                  
  

• Introduces BASiCS_Draw to enable synthetic data generation based on a BASiCS_MCMC object (similar to splatter)

• Style changes to newBASiCS_Data

• Changes in test_data_examples.R to cover all cases.

             Changes in version 1.9.2 (2019-12-04)                  
  

• Adds LazyData: true in DESCRIPTION to pass R CMD Check (R-devel requirement)

• Updates BASiCS_LoadChain to remove dependency to data.table

• Alan added to README.md. Funding acknowledgement updated.

             Changes in version 1.9.1 (2019-11-28)                  
  

• In HiddenBASiCS_MCMC_Start, scran::computeSumFactors was replaced by scran::calculateSumFactors in order to match new version of scran.

batchelor

                    Changes in version 1.4.0                        

• Support the use of arbitrary design matrices in regressBatches().

• Allow lists of objects to be directly passed into the … for many functions.

• Added the clusterMNN() function for performing MNN on cluster centroids.

• Added get.variance= option to fastMNN() to return variance explained from PCA. Support d=NA to skip the PCA step altogether.

• Modified correctExperiments() to preserve non-conflicting rowData() fields.

bayNorm

                   Changes in version 1.5.14                        

• Modify Main_mean_NB_spBay.

                   Changes in version 1.5.13                        
  

• Activate “Allow sparse matrix as output (valid only for mean version procedure)”. Hence you can work on dgCMatrix throughout the process. Input which is not of type dgCMatrix will be converted to dgCMatrix at first.

                   Changes in version 1.5.12                        
  

• Deprecated: Allow sparse matrix as output (valid only for mean version procedure). Since sparse matrix is useful only when the matrix it is sparse.

• Calibrate documentations.

                   Changes in version 1.5.11                        
  

• Allow sparse matrix as output (valid only for mean version procedure).

• Let version of RELEASE_3_10 to be 1.4.11.

                   Changes in version 1.5.10                        
  

• Update RELEASE_3_10 1.4.2 to 1.4.3.

                    Changes in version 1.5.9                        
  

• Change back to Rcpp EstPrior function (sp_mat version).

• Use dgCMatrix instead of matrix in R.

• define ARMA_64BIT_WORD 1 and so on allows for big sparse matrix (learn from the liger R package).

                    Changes in version 1.5.8                        
  

• Change back to rowSums instead of using Rcpp EstPrior function.

                    Changes in version 1.5.7                        
  

• Add useful function file.

• Use Rcpp EstPrior function.

                    Changes in version 1.5.6                        
  

• as_matrix for transforming sparse matrix to matrix in R efficiently than as.matrix.

                    Changes in version 1.5.5                        
  

• Make BB_fun faster: speed up the access of row of dgCMatrix object.

• Modify EstPrior, using rowSums from Matrix package to calculated variance. Hence no need for Rcpp EstPrior function.

                    Changes in version 1.5.4                        
  

• Support sparse matrix: dgTMatrix and dgCMatrix.

                    Changes in version 1.5.3                        
  

• Add Rcpp EstPrior function.

                    Changes in version 1.5.2                        
  

• Vectorize computation in EstPrior function.

                    Changes in version 1.5.0                        
  

• Set default setting of BETA_vec=NULL.

• Update citation.

BEclear

             Changes in version 2.3.1 (2020-03-18)                  

• added helpful output in case the gradient descent diverges

BgeeCall

                    Changes in version 1.2.0                        

• Moved from workflow to software section

                    Changes in version 1.1.1                        
  

• Better manage transcript version

• Manage output directory when calls are generated for several libraries

• Manage transcript version when calls are generated for several libraries

                    Changes in version 1.1.0                        
  

• Change kmer size of kallisto index from 21 to 15 for libraries with readLength <= 50bp

• Can choose the output directory

• By default use a simpler arborescence for the output directory

• Can use reference intergenic sequences generated by the community

• Can use custom reference intergenic sequences from a local fastq file

                    Changes in version 1.0.0                        
  

• Public release of BgeeCall package. Enjoy!!!

BgeeDB

                   Changes in version 2.13.1                        

• Fix issue in the getData() function when trying to uncompress huge tar.gz files (like all human data or GTeX experiment)

bigPint

             Changes in version 1.3.2 (2020-03-04)                  

Users can now input SummarizedExperiment data type to create any bigPint plot.

bioCancer

                   Changes in version 1.15.02                       

• update help page

• rename www/imgs to www/logo: confict with www/imgs of rediant.data package.

                   Changes in version 1.15.01                       
  

• Change the address of reactomeFI from “http://reactomews.oicr.on.ca:8080/” to “http://cpws.reactome.org/”

• update ReactomeFI2018.RDS

BiocCheck

                    Changes in version 1.23                         

BUG FIX

• (1.23.4) Update locations for NEWS

• (1.23.1) Fix False Positive class == check

BiocDockerManager

             Changes in version 0.99.0 (2020-03-18)                 

• Submit to Bioconductor

BiocFileCache

                    Changes in version 1.11                         

BUG FIX

• (1.11.5) Update dplyr functions for dplyr_1.0.0 release

• (1.11.2) Fixes run of examples. Different result manual vs interactive so have conditional that will allow complete example if run by user rather than run automatically through the checks.

NEW FEATURES

• (1.11.1) Add makeCachedActiveBinding(). Allows data to be cached during ActiveBinding call. Avoids callback function executing data retrieval everytime.

• (1.11.3) Only asks for / reports use of temporary cache once per session. https://github.com/Bioconductor/TENxBrainData/issues/7

BioCor

                    Changes in version 1.12                         

• Move to NEWS.md. - Corrected “value of length: 2 type: logical”.

• Avoid cropping the images. - Updated documentation.

                   Changes in version 1.10.1                        
  

• Added a pkgdown website

BiocParallel

                    Changes in version 1.22                         

USER VISIBLE CHANGES

• (v 1.20.2) don’t advance random number stream when used ‘internally’. This behavior alters reproducibility of existing scripts relying (probably implicitly) on the advancing stream. https://github.com/Bioconductor/BiocParallel/issues/110

BUG FIXES

• (v 1.20.1) bplapply(), bpmapply(), bpvec() propagate names on arguments more correctly, https://github.com/Bioconductor/BiocParallel/issues/108

BiocSet

                     Changes in version 1.1                         

BUG FIX

• (1.1.4) Fix tests for release

• (1.1.3) Update dplyr functions in preparation for dplyr 1.0.0 release.

• (1.1.1) Fix tests that test the length of org objects.

NEW FEATURES

• (1.1.2) Allow contruction of sets from lists, BiocSet(list(a=letters, b=LETTERS)).

biocViews

                   Changes in version 1.55.0                        

NEW FEATURES

• (1.55.2) printNEWS and getPackageDescriptions now have argument option ‘relativeLink` that allows for relative links instead of hard coded urls for website. Important for release announcement.

BUG FIX

• (1.55.1) If new package fails to build still include in release announcement and don’t fail out for lack of version number.

biosigner

                   Changes in version 1.15.4                        

MINOR MODIFICATION

• biosigner.Rmd vignette: minor update

                   Changes in version 1.15.2                        
  

NEW FEATURE

• biosigner.Rmd vignette: ropls::view method replaces ropls::strF (deprecated)

biotmle

                   Changes in version 1.11.0                        

• Change of estimation backend from the tmle package to the drtmle package.

• Removal of option to have repeated subjects since unsupported in new backend.

• Adds argument bppar_debug to facilitate debugging around parallelization.

brainflowprobes

                    Changes in version 1.1.1                        

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://LieberInstitute.github.io/brainflowprobes/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

BRGenomics

                   Changes in version 0.99.30                       

• Change all ncores options to default to getOption(“mc.cores”, 2L) - Rename n-dimensional binning functions aggregateByNdimBins() and densityInNdimBins() - Redone documentation website, splitting up the vignette - Updated package vignettes/guide pages in several places - Other minor internal changes

                   Changes in version 0.99.25                       
  

• Bug fixes with expand_ranges arguments affecting getCountsByRegions(), subsampleGRanges(), and getSpikeInNFs() - Expanded testing, particularly for expand_ranges arguments and import_bam() - Added options in mergeReplicates() - Various small doc updates and minor internal changes

                   Changes in version 0.99.23                       
  

• Added support for non-basepair-resolution GRanges throughout, via the expand_ranges argument - Substantial performance benefits for less-sparse datasets (e.g. whole read coverage) - Supported everywhere, including counting functions, subsampling, merging, normalization, etc. - Rewrite of mergeGRangesData(): - Substantial performance improvements for most datasets - No longer requires basepair-resolution GRanges objects - Added options and flexibility for merging reads as well as coverage data - Add a mergeReplicates() function - Rewrite of makeGRangesBRG() that significantly improves performance for sparser datasets (the datasets for which using the function makes the most sense) - subsampleGRanges() no longer returns a basepair-resolution GRanges by default - When field=NULL, applyNFsGRanges() no longer returns a basepair-resolution GRanges by default - Add use_bin_numbers option to n-dimension binning functions; setting to false allows returning of bin values (the bin center) instead of the ordinal bin numbers (indexes) - Quietly adding support for GRangesList objects (not fully tested)

                   Changes in version 0.99.15                       
  

• Add pre-filtering to counting functions for performance - Some additional clarification of readcounts vs. coverage signal in counting and import functions - Change tidyChromosomes test - Remove indirect links in doc pages (use only exact names of man pages)

                   Changes in version 0.99.10                       
  

• Code modifications to pass Bioconductor test builds on Windows: - Make all examples and tests single core - Internally (not exported) redefine mcMap (current implementation in package parallel needs to be modified) - In tests and examples, test if on Windows before attempting any bigWig file import

                   Changes in version 0.99.0                        
  

• Changes for Bioconductor submission: - Move to package versioning 0.99.x - Update R requirement to version 4.0 - Add new branch R3 to allow users to install under R version >=3.5 - Various minor formatting changes to codebase

                    Changes in version 0.8.1                        
  

• Fixed bug in import_bam() that produced warnings when shift argument used to shift both 5’ and 3’ ends of reads (i.e. when length(shift) == 2) - Updated included external datasets to be much smaller - Included bam file now <200 reads - Included bigWig and bedGraph files derived from the bam file - Minor update to vignette to reflect the change in the bam file - Updated the included data() objects (PROseq and PROseq_paired) - Shifted PRO-seq 3’ bases to remove the run-on base, and updated associated package tests - Added xz compression to the files - Streamlined some method dispatch in genebodies() and getDESeqDataSet() functions

                    Changes in version 0.8.0                        
  

• Add support for lists in data import functions - Add the convenience function applyNFsGRanges() - Significant internal changes to import_bam() - New test for paired-end reads (deprecated use of Rsamtools::testPairedEndBam()) - Avoids any internal use of bpiterate() - Dropped dependency on GenomicFiles package

                   Changes in version 0.7.10                        
  

• Add intersectByGene() and reduceByGene() functions - Minor vignette updates

                    Changes in version 0.7.8                        
  

• Substantially updated vignette - Fully load rtracklayer (so completely exported to users) - Add isBRG() function - Fixed bug in spikeInNormGRanges() that failed to remove spike-in reads (aside from maintaining those reads, normalization was otherwise correct) - Fixed minor bug in which metaSubsample() automatically added rownames with list input

                    Changes in version 0.7.7                        
  

• Bug fix in aggregateByNdimensionalBins() affecting simultaneous aggregation of multiple data - Minor updates to documentation, including an error in getDESeqResults() - Slightly expanded vignette

                    Changes in version 0.7.5                        
  

• Update bootstrapping functions - Add blacklisting support for metaSubsample() - Related to blacklisting, NA values now ignored in bootstrapping - Add additional melt options for signal counting functions - Further expanded support for list inputs (lists of GRanges datasets), including in getStrandedCoverage() - Add explicit support for blacklisting in getDESeqDataSet() - Rewrite n-dimensional binning functions, and add function for aggregating data within n-dimensional bins - Changed arguments in binNdimensions() to only accept dataframe inputs - Add densityInNdimensionalBins() function to count points in each bin - Add aggregateByNdimensionalBins() function to aggregate data within bins using arbitrary functions - Added arguments for setting sample names in spike-in/normalization functions - Various improvements and streamlining for method dispatch and flexibility

                    Changes in version 0.7.0                        
  

• Added functions for counting and filtering spike-in reads - Added functions for generating spike-in normalization factors - Added support for lists of GRanges datasets throughout, including all signal counting functions - Updating signal counting functions with a blacklist argument, for ignoring reads from user-supplied regions - Added wrappers for import_bam() for several common use cases - Update getCountsByPositions(): - Added a melt option for returning melted dataframes - Now returns an error by default if multi-width regions are given (must be explicit) - Changed argument order in getMaxPositionsBySignal()

                    Changes in version 0.5.6                        
  

• Update import_bam() function - Added support for paired-end bam files - Added the shift argument - Made metaSubsample() functions robust to unevaluated inputs - Small performance improvement to genebodies() function - Multicore usage is again the default for getDESeqResults()

                    Changes in version 0.5.3                        
  

• Substantial performance improvement for mergeGRangesData() - Make single-core the default for getDESeqResults() - Fixed errant warning message in binNdimensions() for integer inputs - Update namespace to fully import GenomicRanges and S4Vectors - Changed R dependency, evidently required by the updated data objects - Various documentation updates - Added package documentation page - Minor changes to examples

                    Changes in version 0.5.0                        
  

• Increased support for multiplexed GRanges objects across all functions - Increased performance for bootstrapping over multiple fields/multiplexed GRanges objects - Removed requirement to set ‘field’ argument for gettings counts over multiplexed GRanges

                    Changes in version 0.4.7                        
  

• Rewrote mergeGRangesData() to support the creation of multiplexed GRanges objects - Made getCountsByRegions() and getCountsByPositions() to return integers if input signal is integer

                    Changes in version 0.4.5                        
  

• Added and modified numerous arguments - Increased support for normalization factors across signal counting functions - Modified behavior of bootstrapping over multiple fields by removing explicit access to .Random.seed

                    Changes in version 0.4.1                        
  

• Various documentation updates

                    Changes in version 0.4.0                        
  

• Added a NEWS.md file to track changes - Added support for bam files

BridgeDbR

                   Changes in version 1.21.6                        

NEW FEATURES

• adds a getProperties() method

• adds a maps() method that can map multiple identifiers

SIGNIFICANT USER-LEVEL CHANGES

• the map() method now returns a data frame

                   Changes in version 1.21.5                        
  

BUG FIXES

• fixed links in the Vignette and some further clarification

                   Changes in version 1.21.4                        
  

BUG FIXES

• updated the Apache Derby library to 10.5.3.0 (fixing compatibility with newer ID mapping databases)

• replaced RCurl with curl to fix downloading on Windows

                   Changes in version 1.21.3                        
  

BUG FIXES

• force RCurl to use TSL1.2

• added clarification of external data sources used

                   Changes in version 1.21.2                        
  

BUG FIXES

• updated URL of the /data/gene_database/ location to point directly to bridgedb.github.io

• now uses the smaller Bs mapping database as test data in the example

• updated the code for getDatabase() to allow downloading data from any location provided by /data/gene_database/

                   Changes in version 1.21.1                        
  

BUG FIXES

• no longer tries to get Derby file names online

BUSpaRse

             Changes in version 1.1.4 (2020-04-23)                  

• Now tr2g_* functions can also extract transcriptomes. - By default, tr2g_* functions write the tr2g.tsv to disk. - Write filtered GTF and GFF3 files. - List of available gene and transcript biotypes from Ensembl can be queried by data(). - RefSeq GFF3 annotations can now be used in tr2g_gff3.

             Changes in version 1.1.3 (2020-04-06)                  
  

• Allow filtering gene and transcript biotypes in tr2g and get_velocity_files - Allow removing scaffolds and haplotypes from genome annotations for tr2g

             Changes in version 1.1.2 (2020-02-06)                  
  

• Removed RcppParallel and data.table dependencies, and hence all C++ multithreading - Added knee_plot function - Changed default in read_count_output to tcc = FALSE

             Changes in version 1.1.1 (2020-01-29)                  
  

• Sort GRanges for RNA velocity to make sure that exons are in the right order; split no longer sorts within each element of GRangesList. - Export subset_annot, which makes sure that all chromosomes in the annotation are present in the genome prior to transcriptome extraction.

CAGEfightR

                    Changes in version 1.7.5                        

• MAJOR/BREAKING UPDATE: quantifyCTSSs is now a generic with new defaults. When importing BigWig files, tiles are no specifed as a single number of tiles across the genome, rather than size in basepairs. The new default is to import the entire genome as a single tile. This should be the fastest option for small datasets, for larger datasets is usually faster to use multiple tiles.

• quantifyCTSSs now accepts bedGraph files. Unlike BigWig import, this works on Windows.

• New convert*-family of functions which can convert CTSSs between BigWig/BED/bedGraph formats.

• New checkCTSSs for checking whether CTSSs-files are correctly formatted, and if not, will hopefully output some useful diagnostics.

• New quickGenes wrapper function for collapsing cluster-level data to gene-level data. Check the vignette for example of usage.

• New shapeMean function.

• Many internal functions are now exposed as utils*-function. This should make it easier for power users and/or developers to modify and extend CAGEfightR.

• Some internal changes to quantifyCTSSs and quantifyClusters for slightly better performance.

• Fixed a small bug where assignGeneID counted NA as a gene when outputting a message. Note, this never affected the actual output of the function, just the message produced.

CAGEr

                   Changes in version 1.30.0                        

BUG FIXES

• Correct usage of && for vector comparison in pairs.DataFrame().

• Adjust to latest SummarizedExperiment MultiAssayExperiment versions.

CAMERA

                   Changes in version 1.43.2                        

BUG FIXES

• Change several && causing failure with R_CHECK_LENGTH_1_CONDITION and R_CHECK_LENGTH_1_CONDITION

                   Changes in version 1.43.1                        
  

BUG FIXES

• Improve vignette layout and fix typos, thanks to Anton Nikolas Waniek

Cardinal

                   Changes in version 2.5.12                        

BUG FIXES

• Drawing a region-of-interest using ‘selectROI()’ should now update the plot properly in RStudio devices

• Fixed issues with automatically guessing a reasonable mass tolerance for certain pre-processing methods

• In ‘mzBin()’, the previous value of ‘centroided()’ from the original dataset is now preserved after binning

                   Changes in version 2.5.11                        
  

BUG FIXES

• Fixed bug in ‘spatialShrunkenCentroids()’ that produced in NaNs when discriminant scores were very large

• Fixed bug in ‘spatialFastmap()’ where subsetting produced vectors instead of matrices due to omitting ‘drop=FALSE’

                   Changes in version 2.5.10                        
  

NEW FEATURES

• Added ‘topFeatures()’ method for ‘spatialKMeans()’

• Added coercion to ‘DataFrame’ from ‘MSImagingExperiment’

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecated legacy classes (MSImageSet, etc.): class definitions will remain for supporting datasets from CardinalWorkflows, but methods operating on them will be defunct in BioC 3.12

                    Changes in version 2.5.9                        
  

NEW FEATURES

• Added ‘aggregate()’ method for imaging experiments including ‘summarizePixels()’ and ‘summarizeFeatures()’

• Added ‘subset()’ method for imaging experiments including ‘subsetPixels()’ and ‘subsetFeatures()’

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecated ‘dplyr’ verbs in favor of the above functions; this is to remove the (rather large) dependency on the tidyverse for a relatively small functionality

BUG FIXES

• Fix bug in ‘spatialDGMM()’ printing caused by a change in default.stringsAsFactors() == FALSE in R 4.0

                    Changes in version 2.5.8                        
  

NEW FEATURES

• Automatic estimation of mass resolution will now work for ‘processed’ imzML with centroid spectra

• New getter/setter options for Cardinal options such as ‘getCardinalBPPARAM()’ and ‘setCardinalBPPARAM()’

SIGNIFICANT USER-VISIBLE CHANGES

• Default BPPARAM backend is now set to ‘SerialParam()’; use ‘setCardinalBPPARAM()’ to change the backend

• Expose ‘.view’ argument of ‘matter::chunk_apply()’ in ‘pixelApply()’, ‘featureApply()’, and ‘spatialApply()’

• Previously-deprecated functions ‘generateSpectrum()’ and ‘generateImage()’ are now defunct

• Removed defunct functions ‘Binmat()’ and ‘topLabels()’

BUG FIXES

• Fix large intensity text cutoffs in ‘image()’ colorkey

                    Changes in version 2.5.7                        
  

BUG FIXES

• Fix bug when using ‘rbind()’ or ‘cbind()’ on ‘MassDataFrame’ and ‘PositionDataFrame’

                    Changes in version 2.5.6                        
  

BUG FIXES

• Fix bug when assigning a dense matrix via iData()<- for an ‘MSProcessedImagingExperiment’ object

                    Changes in version 2.5.5                        
  

BUG FIXES

• Fix bug in ‘show’ method for ‘SimpleImageList’ caused by class(matrix) -> c(“matrix”, “array”)

                    Changes in version 2.5.4                        
  

BUG FIXES

• Fix bugs in legacy classes caused by a change in default.stringsAsFactors() == FALSE in R 4.0

                    Changes in version 2.5.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The ‘resolution’ argument in all methods has been redefined to always mean **full bin widt for both “mz” and “ppm” units

                    Changes in version 2.5.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The ‘pixelApply()’, ‘featureApply()’, and ‘spatialApply()’ methods now internally use ‘matter::chunk_apply()’

                    Changes in version 2.5.1                        
  

BUG FIXES

• Fixed bug in ‘mzBin()’ binning spectra incorrectly

• Fixed bug in contrast enhancement with missing intensities

cbaf

             Changes in version 1.10.0 (2020-04-08)                 

New Features

• A unified method for increasing the consistency of cancer terms used by various functions. This enables easier maintanance and faster inclusion of new terms whenever available.

• Terms are updated. Package can recongize even more cancer studies!

• Incluion of additional checkpoint to control the name of requested cancer studies.

CellBench

                    Changes in version 1.3.2                        

Bug Fixes

• apply_methods and time_methods now correctly produces results for custom data.frames whose columns are not sorted from left to right

CellMixS

                    Changes in version 1.3.7                        

• Add input checks for colnames

• Include score and warning for identical cells

ceRNAnetsim

            Changes in version 0.99.16 (2019-11-20)                 

• Fixed documentation fails

• Re-arranged vignettes

             Changes in version 0.99.0 (2019-10-07)                 
  

• Submitted to Bioconductor

CeTF

                   Changes in version 0.99.19                       

• Fix netGOTFPlot, RIFPlot and densityPlot functions

• Fix warning messages when ploting with ggplot2 package (densityPlot, enrichPlot, histPlot, RIFPlot, SmearPlot)

                   Changes in version 0.99.18                       
  

• Fix SmearPlot bugs.

                   Changes in version 0.99.17                       
  

• Updating citation.

• Adding CITATION file.

                   Changes in version 0.99.16                       
  

• Development version.

• Fix netGOTFPlot dependencies and add the label size parameter.

• Update vignette.

                   Changes in version 0.99.15                       
  

• Development version.

• Adding ‘level’ parameter to perform groupGO analysis in getGroupGO function.

• Adding getEnrich function.

• Adding enrichPlot and heatPlot function.

• Adding RIFPlot function.

• Adding diffusion function.

• Adding CircosTargets function.

• Fix netGOTFPlot function bugs.

• Updated vignette.

ChAMP

                   Changes in version 2.17.3                        

• Fixed bug in runCombat, as some factors are numeric format.

ChemmineR

                   Changes in version 3.40.0                        

NEW FEATURES

• Prior to this version, V3000 sdf files could be read, but would be written back out in V2000 format. Now these files will be written back out as V3000 files.

ChIPpeakAnno

                   Changes in version 3.21.7                        

• Fix a potentical bug reported by millerh1.

                   Changes in version 3.21.6                        
  

• add new function findMotifsInPromoterSeqs. HANGES IN VERSION 3.21.5

• replace all class by is.

                   Changes in version 3.21.4                        
  

• Fix a bug in getAllPeakSequence when there is peak out side of genome.

                   Changes in version 3.21.3                        
  

• Update function summarizePatternInPeaks.

                   Changes in version 3.21.2                        
  

• Add function getGO.

                   Changes in version 3.21.1                        
  

• remove RangedData from ChIPpeakAnno.

ChIPseeker

                   Changes in version 1.23.1                        

• update GEO data (51079/762820 GSM) (2019-12-20, Fri)

chromstaR

                   Changes in version 1.13.1                        

BUG FIXES

• Compatibility update: Replaced deprecated fetchExtendedChromInfoFromUCSC() with getChromInfoFromUCSC().

CHRONOS

                   Changes in version 1.15.1                        

• Updates for R_CHECK_LENGTH_1_LOGIC2, R_CHECK_LENGTH_1_CONDITION, classEq.

CiteFuse

                   Changes in version 0.99.7                        

• Improved Vignettes - Add examples - Fix for BiocCheck - Remove Rcpp implementation

cleaver

             Changes in version 1.25.1 (2019-12-30)                 

• Add missing space in vignette.

CluMSID

                    Changes in version 1.3.1                        

• fixed bug in mergeMS2spectra when used with external peaktable

clusterExperiment

                    Changes in version 2.7.2                        

Bugs:

• Fix error from R 4.0 changing definition of treatment of NULL (“For consistency, N <- NULL; N[[1]] <- val now turns N into a list also when val) has length one. This enables dimnames(r1)[[1]] <- “R1” for a 1-row matrix r1, fixing PR#17719 reported by Serguei Sokol.”). Replaced all <- c() with <- vector(...) and the appropriate class.

                    Changes in version 2.7.1                        
  

Bugs:

• Fix error in making sample dendrogram

clusterProfiler

                   Changes in version 3.15.3                        

• incorporate clusterProfiler.dplyr (2020-03-12, Thu) - arrange, filter, group_by, mutate, rename, select, slice and summarize

                   Changes in version 3.15.2                        
  

• remove Suggests of KEGG.db as it will be deprecated in Bioconductor 3.11 (2020-01-14, Tue) - optimize enrichGO to use less memory (2019-12-13, Fri) - re-implement read.gmt without using GSEABase, and my own version is much more fasta :)

                   Changes in version 3.15.1                        
  

• e.g. user can pass fun=enrichGO to compareCluster without quoting enrichGO (2019-12-02, Mon) - add keytype and readable info in compareCluster output - mv compareClusterResult class defintion to DOSE (2019-11-02, Sat) - mv fortify, barplot and dotplot for compareClusterResult to enrichplot.

clustifyr

             Changes in version 0.99.0 (2019-11-06)                 

• Update to tutorials

• bug fixes

• cleanup for bioc

             Changes in version 0.0.3 (2019-09-06)                  
  

• support of SingleCellExperiment objects and more

• bug fixes

             Changes in version 0.0.2 (2019-05-29)                  
  

• Updated discussions, benchmark, and visualization example pages

• reorganized clustifyrdata data package

             Changes in version 0.0.1 (2019-02-01)                  
  

• Added direct support for seurat and other object classes

• Updated readme and tutorial pages

• Moved some larger reference data to clustifyrdata

cmapR

             Changes in version 0.99.0 (2020-01-13)                 

• NOTE: updated function names replacing ‘.’ with ‘_’ (ex: ‘parse_gctx’)

• Submitted to Bioconductor

CNVfilteR

                    Changes in version 1.1.6                        

SIGNIFICANT USER-VISIBLE CHANGES

• plotVariantsForCNV() allows multiple visual adjustements

MINOR

• Added error control in loadVCFs(): heterozygous.range and homozygous.range cannot overlap

                    Changes in version 1.1.5                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Added ignore.unexpected.rows parameter to loadCNVcalls() function to ignore CNV calls which deletion/duplication value is not the expected one.

BUG FIXES

• Some SNV callers can produce calls with a genotype indicating that the variant actually was not found. Variants with GTs like “0/0 ./. 1/0” are now discarded.

• Certain SNV callers can produce SNV calls with more than two alt values (multiple alt alleles). These variants are now discarded.

                    Changes in version 1.1.4                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Improved CNVfilteR accuracy. margin.pct parameter was added to filterCNVs() and ht.deletions.threshold default value was modified to 30.

• Loading variants process optimized (multiple times faster)

• filterCNVs() function optimized

• min.total.depth default value modified to 10

• Added multiple modifications to the vignette

BUG FIXES

• Fixed bug when plotting a CNV with no SNV variants falling in it

                    Changes in version 1.1.3                        
  

BUG FIXES

• Fixed bug when processing variants in the limits of heterozygous.range and heterozygous.range

                    Changes in version 1.1.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Added sample.name parameter to loadCNVcalls() function to allow explicitly setting sample name

• deletion and duplication parameters can be vectors in loadCNVcalls() function, so multiple values are allowed

BUG FIXES

• Fixed bug happening in loadSNPsFromVCF() when ref and alt support was 0

• Fixed bug when processing list.support.field in loadSNPsFromVCF()

• Added error control when allele frequency is not numeric

• Minor fixes

CNVPanelizer

                   Changes in version 1.19.1                        

• Fix due to change of Matrix class type in R version 4

CNVRanger

                    Changes in version 1.4.0                        

• New function cnvOncoPrint to visualize CNV calls on overlapping genomic features across a sample population

cogena

             Changes in version 1.21.2 (2020-04-21)                 

• update coExp for R4.0 due to Matrix is now Array.

cola

                    Changes in version 1.3.2                        

• add a new vignette introducing functional enrichment

combi

                   Changes in version 0.99.9                        

• Removed bplapply functionality because of Windows errors

                   Changes in version 0.99.7                        
  

• Created a print method for combi objects - Stricter argument checking for exported functions - Consequent naming of results

                    Changes in version 0.1.2                        
  

• Reduce build time using

                    Changes in version 0.1.0                        
  

• First private GitHub document

compcodeR

                   Changes in version 1.23.1                        

• Moved vignette to Rmd

ComplexHeatmap

                    Changes in version 2.3.4                        

• add alter_graphic() to automatically generate alteration graphic functions.

• add label/annotation_label argument in SingleAnnotation() and HeatmapAnnotation().

• improved the subsetting methods for comb_mat class

• rewrite smartAlign2()

                    Changes in version 2.3.3                        
  

• support gridtext package

• fixed the bug of node stack overflow when there are many identical rows for drawing the dendrogram. see (http://www.thinkingincrowd.me/2016/06/06/How-to-avoid-Stack-overflow-error-on-recursive/)

• support to set legend gaps

• print important messages, e.g. when number of rows are more than 2000, interanlly use_raster is turned on and the message should be printed to users.

• UpSet plots: optimize the processing of many sets (current solution consumes huge memory)

• UpSet plots: the “intersect” and “union” modes are currectly calculated.

• anno_block(): add show_name argument.

                    Changes in version 2.3.2                        
  

• anno_simple(): fixed a bug when pch are all NA in a slice

• adjust code according to grid 4.0.

• move scripts in test_not_run/ to tests/ folder

• Heatmap(): cluster_row_slice/cluster_column_slice set to TRUE by default for character matrix and when dendrogram is already provided.

• smartAlign2(): improved the code that positions are correctly calculated.

• row titles are in the correct order if they are set as “template”.

                    Changes in version 2.3.1                        
  

• anno_points(): allows images as symbols.

• add HEATMAP_LEGEND_PADDING and ANNOTATION_LEGEND_PADDING options in ht_opt

• oncoPrint(): print messages if there are NA values in the input matrix

ConsensusClusterPlus

Changes in Version 1.52.0

• Brief R code update for compatibilty with R 4.0.
• Improved messages.
• Deprecated kmdist clustering option

consensusDE

             Changes in version 1.5.1 (2019-12-03)                  

• strand_mode argument replaces ignore_strand in buildSummarized.

• fragments default in buildSummarized changed to FALSE

• update vignette

CoreGx

                    Changes in version 1.0.0                        

• Implemented molecularProfiles as SummarizedExperiments instead of ExpressionSets - Modifying generic implementation to add …; allows for additional arguments in setMethods() for CoreGx generics - Removing package from CRAN] - Submitting package to Bioconductor

csaw

                   Changes in version 1.22.0                        

• Removed deprecated functionality in consolidateTests() and related functions.

• Modified the method used to count the number of up/down windows in combineTests(). Reported a representative test in the output along with its log-fold changes.

• Renamed mixedClusters() to mixedTests() with deprecation of the former.

• Added minimalTests() for cluster-level summarization with a minimum proportion of significant tests.

• Standardized the output of getBestTest(), empiricalFDR(), mixedTests() and minimalTests() to that of combineTests(). In particular, getBestTest() now returns the index of its best window in the rep.test field.

ctgGEM

             Changes in version 0.99.0 (2020-01-07)                 

• submitted to Bioconductor

customProDB

                   Changes in version 1.26.1                        

BUG FIXES

• Fix a small bug in function PrepareAnnotationRefseq.R

cydar

                   Changes in version 1.12.0                        

• prepareCellData() now returns a List rather than a half-complete CyData object.

• expandRadius() and neighborDistances() work explicitly on the List produced by prepareCellData().

• countCells() will compute weighted-median intensities for unused markers as well. Minor bugfix to avoid stochastic results due to numerical imprecision when computing medians.

• intensities() has a new mode= argument to return intensities for unused markers.

cytomapper

             Changes in version 0.99.5 (2020-04-10)                 

• Added script to generate the toy dataset

• Modified the toy dataset

• Added more explanation on datasets to vignette

• Bug fixes when colouring cells

• Unit tests on all hidden functions

• Account for over-saturation when merging colours

• Fixed labelling of colour legends

• Corrected typos in docs and vignette

• Avoid recalculation of min/max values in legend function

             Changes in version 0.99.4 (2020-04-01)                 
  

• Fixed docs to pass checks on Windows

• Aesthetic changes to scale bar, image title and legend title

• Removed channelNames as Image generic

• removed exported plot method

             Changes in version 0.99.0 (2020-03-30)                 
  

• Formatted the package for Bioconductor submission

             Changes in version 0.1.13 (2020-03-28)                 
  

• Full vignette and correction to docs

             Changes in version 0.1.12 (2020-03-25)                 
  

• Renamed package from SingleCellMapper to cytomapper

• Renamed ImageList class to CytoImageList class

             Changes in version 0.1.11 (2020-03-24)                 
  

• Complete documentation of all package functions

             Changes in version 0.1.10 (2020-03-21)                 
  

• interpolate parameter

• Bug fix to achieve correct aspect ratios

             Changes in version 0.1.9 (2020-03-20)                  
  

• scale, return_plot, return_images, legend, margin, display parameters

• Finalised unit tests

             Changes in version 0.1.8 (2020-03-18)                  
  

• Option to remove legend

• Cleaned up representation of legend on plot

             Changes in version 0.1.7 (2020-03-17)                  
  

• Added scaleImages and normalize functions

• Expanded shared parameters for plotPixels and plotCells

             Changes in version 0.1.6 (2020-03-10)                  
  

• Unit tests on plotCells and plotPixels

• Improved setting colours

• Rewrite to reduce validity checks

             Changes in version 0.1.5 (2020-03-03)                  
  

• plotCells function

• plotPixels function

• Options for further customization of scale_bar

• Options for image_title customization

• Started vignette draft

             Changes in version 0.1.4 (2020-02-16)                  
  

• Full docs and test on: - loadImages - ImageList-class

             Changes in version 0.1.3 (2020-02-16)                  
  

• Full docs and tests on: - ImageList-naming - ImageList-subsetting

             Changes in version 0.1.2 (2020-02-03)                  
  

• channelNames generic function for Image and ImageList object

• Reduced the size of example data

• Wrote docs on data

             Changes in version 0.1.1 (2020-02-02)                  
  

• Simplified structure of loadImages function

• Created validity checks for path and file inputs

• Fixed bugs to pass R CMD check

• test

             Changes in version 0.1.0 (2020-01-16)                  
  

• Initial commit

• Creation of the SingleCellMapper package

• Created inst/extdata folder with example images and data

• Build the ImageList class

• Created first unit tests for ImageList constructor

• test

CytoML

                    Changes in version 3.11                         

API Changes

• Rename argument sampNLoc -> sample_names_from in open_flowjo_xml - All parsers (flowjo/cytobank/diva_to_gatingset) now return GatingSet based on cytoset rather than ncdfFlowSet - Add trans argument to cytobank_to_gatingset to allow overriding of transformations from gatingML file (#76) - gatingset_to_flowjo now uses a docker image with a compiled converter: hub.docker.com/r/wjiang2/gs-to-flowjo - Some updates to how flowjo_to_gatingset searches for FCS files (#77)
• Add include_empty_tree option to flowjo_to_gatingset to include samples without gates - Allow gatingset_to_flowjo to take a path to a GatingSet archive directory - Add gating_graphGML to replace gating.graphGML method for openCyto::gating generic - Filter samples by panel when parsing cytobank experiment and add ce_get_samples, ce_get_panels

Fixes/internal changes

• Automatic time scaling of samples from FlowJo workspaces now handled by flowjo_to_gatingset RGLab/cytolib#33 - Handle change to default stringsAsFactors=FALSE in R 4.0 - Eliminated extra intermediate files left in temp directory during workspace parsing - Switch usage of GatingSetList to merge_gs_list - Solve some Windows build issues - Switch from experimental::filesystem to boost::filesystem in C++ FlowJo parser - Add CytoML XSD to installation

                    Changes in version 3.10                         
  

API Changes

• Change handling of quad gates according to RGLab/cytolib#16

• Renaming of methods:

• openWorkspace -> open_diva_xml, open_flowjo_xml - cytobankExperiment -> open_cytobank_experiment - cytobank2GatingSet -> cytobank_to_gatingset - parseWorkspace -> flowjo_to_gatingset, diva_to_gatingset - getSampleGroups -> fj_ws_get_sample_groups, diva_get_sample_groups - getSamples -> fj_ws_get_samples, diva_get_samples - getKeywords -> fj_ws_get_keywords - getCompensationMatrices -> ce_get_compensations - getTransformation -> ce_get_transformations - compare.counts -> gs_compare_cytobank_counts

• Renaming of classes:

• divaWorkspace -> diva_workspace - flowJoWorkspace -> flowjo_workspace

• Add CytoML.par.set, CytoML.par.get for setting parameters in CytoML namespace

Fixes/internal changes

• Make gatingset_to_cytobank export cytobank ML with attribute namespaces - Allow diva_to_gatingset to use compensation matrix from xml - Pass … args from cytobank_to_gatingset appropriately down to FCS parser - Fix some issues with scaling of gates parsed from Diva workspace (#64) - Guard against unsupported transformations being added to GatingSet during Diva parsing - Switch diva_to_gatingset to using flowjo_log_trans instead of logtGml2_trans - Fix ported flowUtils::xmlTag to enable self-closing tags - Make gating.graphGML lookup tailored gates by FCS name as well as file id - Add some flexibility to getSpilloverMat used in gatingset_to_flowjo

DAMEfinder

                   Changes in version 0.99.3                        

• Change some files to other folders

                   Changes in version 0.99.2                        
  

• Fix spacing (ggplot code looks funky now)

• Remove make_bigwigs func

• Fix examples for plotting functions

                   Changes in version 0.99.1                        
  

• Fix description file

                   Changes in version 0.99.0                        
  

• First version submitted to Bioconductor

                    Changes in version 0.2.0                        
  

• New SNP-based ASM score. Includes VCF and BAM files as input.

• New p-value assignment methods.

• New plotting functions for MDS and Methyl-circle-plots.

                   Changes in version 0.1.13                        
  

• Last version before S.Orjuela started working on it.

DaMiRseq

                    Changes in version 2.0.0                        

• Since version 2.0.0 of the software, DaMiRseq offers a solution to solve two distinct problems, in supervised learning analysis: (i) finding a small set of robust features, and (ii) building the most reliable model to predict new samples;

• The functions DaMiR.EnsembleLearning2cl_Training, EnsembleLearning2cl_Test and EnsembleLearning2cl_Predict were deprecated and replaced by DaMiR.EnsL_Train, DaMiR.EnsL_Test and DaMiR.EnsL_Predict, respectively;

• We have created a new function DaMiR.ModelSelect to select the best model in a machine learning analysis;

• We have created two new functions DaMiR.iTSnorm and DaMiR.iTSadjust to normalize and adjust the gene espression of independent test sets;

• Two types of expression value distribution plot were added to the DaMiR.Allplot function.

dearseq

             Changes in version 1.0.0 (2019-11-26)                  

• this is a reboot of the tcgsaseq package

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

• A few changes to shearwater vignette

• Renamed arguments pi.gene and pi.backgr in makePrior()

Bugfixes

• Fixed bug in bf2Vcf() when no variant is called

             Changes in version 1.99.2 (2013-07-11)                 
  

Updates

• Updated CITATION

• Added verbose option to bam2R to suppress output

• Changed mode() to “integer” for value of loadAllData()

Bugfixes

• Fixed bug when only one variant is called in bf2Vcf()

             Changes in version 1.99.1 (2013-06-25)                 
  

Updates

• Using knitr for prettier vignettes

• Including shearwater vignette

Bugfixes

• fixed issues with deletions in bf2Vcf()

• makePrior() adds background on all sites

             Changes in version 1.99.0 (2013-04-30)                 
  

Updates

• New shearwater algorithm

• Including VCF output through summary(deepSNV, value=”VCF”)

DEGreport

                   Changes in version 1.23.3                        

• Fix: pass min_counts parameter to degPlotCluster

                   Changes in version 1.23.2                        
  

• Fix: adopt class(counts)1 to check classes

                   Changes in version 1.23.1                        
  

• Feature: add prefix to clusters plot in degPlotCluster

DelayedArray

                   Changes in version 0.14.0                        

NEW FEATURES

• Support ‘type(x) <- new_type’ to change the type of a DelayedArray object.

• 1D-style single bracket subsetting of DelayedArray objects now supports subsetting by a numeric matrix with one column per dimension.

SIGNIFICANT USER-VISIBLE CHANGES

• No more parallel evaluation by default, that is, getAutoBPPARAM() now returns NULL on a fresh session instead of one of the parallelization backends defined in BiocParallel. It is now the responsibility of the user to set the parallelization backend (with setAutoBPPARAM()) if they wish things like matrix multiplication, rowsum() or rowSums() use parallel evaluation again. Also BiocParallel has been moved from Depends to Suggests.

• Replace arrayInd2() and linearInd() with Lindex2Mindex() and Mindex2Lindex(). The new functions are implemented in C for better performances and they properly handle L-index values greater than INT_MAX (2^31 - 1) in the input and output.

• 2x speedup to coercion from DelayedArray to SparseArraySeed or dgCMatrix.

DEPRECATED AND DEFUNCT

• arrayInd2() and linearInd() are now deprecated in favor of Lindex2Mindex() and Mindex2Lindex().

BUG FIXES

• Fix handling of linear indices >= 2^31 in 1D-style single bracket subsetting of DelayedArray objects.

• rowsum() & colsum() methods for DelayedArray objects now respect factor level ordering (issue #59).

• Coercion from DelayedMatrix to dgCMatrix now propagates the dimnames.

• No more quotes around the NA values of a DelayedArray of type “character”.

• Better error message when Ops methods for DelayedArray objects reject their operands.

DeMixT

                    Changes in version 1.2.5                        

• Added pi01 and pi02 as input values for users to initialize the proportion estimation.

• Added nspikein as an input value in the DeMixT, DeMixT_S1 and DeMixT_GS functions to specify how many spike-in normal reference samples need to be generated; Setting nspikein at null as a default value, the number of spike-in normal reference samples equal the min(200, 0.3 x My), where My is the number of mixed samples; By setting nspikein equals 0, no spike-in normal reference will be generated; If the input value of data.N2 is not null, nspikein will be forced to be 0.

• Added DeMixT_GS function, new proposed gene selection method which applies profile likelihood, for proportion estimation.

• Added simulate_2comp function for users to simulate test data for 2-component de-convolution.

• Added simulate_3comp function for users to simulate test data for 3-component de-convolution.

• Added row names and column names for all output values.

• Added gene.selection.method as an input value for DeMixT function. The default is ‘GS’.

• Added ngene.Profile.selected as an input value for DeMixT function. The default is NA.

DepecheR

             Changes in version 1.3.3 (2020-03-18)                  

• Hiearchical clustering and ordering of the columns in the Cluster_centers heatmap from depeche.

• Note fixed regarding the use of ::: in GroupStatPlot

             Changes in version 1.3.2 (2020-02-05)                  
  

• Bug fix in groupProbPlot solving issues when the cell number is low.

• Update of dWilcox.

             Changes in version 1.3.1 (2019-12-05)                  
  

• Vinjette changes o Introduction of a vinjette for the groupProbPlot function. o Fixing a minor bug in the general vinjette.

derfinder

                   Changes in version 1.21.7                        

BUG FIXES

• Noticed an issue with GenomicState::gencode_genomic_state() that ultimately was due to makeGenomicState() and the transition in R to have as default data.frame(stringsAsFactors = FALSE) instead of TRUE.

                   Changes in version 1.21.5                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Now makeGenomicState() now restores the GenomicFeatures::isActiveSeq() on the txdb object before finishing to avoid issues, like running regionReport::renderReport() on two different sets of regions (different chrs). There’s a new unit test for this.

BUG FIXES

• Removed knitrBootstrap citation code. - Made a test less susceptible to numerical precision.

                   Changes in version 1.21.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://lcolladotor.github.io/derfinder/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

                   Changes in version 1.21.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Use GenomeInfoDb::getChromInfoFromUCSC() when possible instead of data from biovizBase::hg19Ideogram for getting the hg19 chromosome lengths.

derfinderHelper

                   Changes in version 1.21.1                        

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://leekgroup.github.io/derfinderHelper/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

derfinderPlot

                   Changes in version 1.21.4                        

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://leekgroup.github.io/derfinderPlot/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

                   Changes in version 1.21.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Code in all examples has been re-styled thanks to styler::style_pkg(), see dev/02_update.R for details.

                   Changes in version 1.21.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Switched from Travis to GitHub actions through usethis. - Build the documentation website automatically with pkgdown. - Added a dev/01_setup.R script. - Now using a README.Rmd file.

                   Changes in version 1.21.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Use GenomeInfoDb::getChromInfoFromUCSC() when possible instead of data from biovizBase::hg19Ideogram for getting the hg19 chromosome lengths.

DESeq2

                   Changes in version 1.28.0                        

• For lfcShrink(), changed order of type options: “normal” will no longer be first, as it under-performed “apeglm” and “ashr” in Zhu et al (2018). The new order is type=c(“apeglm”, “ashr”, “normal”).

• Added arguments to estimateDispersions: useCR (logical), and weightThreshold (numeric, default of 1e-2). The first argument optionally avoid the calculation of Cox-Reid adjustment term. The second argument sets the threshold for subsetting the design matrix and GLM weights when calculating the adjustment term. In addition, baseMean uses weights when calculating the mean of normalized counts, if weights matrix is provided.

                   Changes in version 1.27.12                       
  

• For lfcShrink(), changed order of type options: “normal” will no longer be first, as it under-performed “apeglm” and “ashr” in Zhu et al (2018). The new order is type=c(“apeglm”, “ashr”, “normal”).

                   Changes in version 1.27.9                        
  

• Added arguments to estimateDispersions: useCR (logical), and weightThreshold (numeric, default of 1e-2). The first argument optionally avoid the calculation of Cox-Reid adjustment term. The second argument sets the threshold for subsetting the design matrix and GLM weights when calculating the adjustment term. In addition, baseMean uses weights when calculating the mean of normalized counts, if weights matrix is provided.

DEsubs

                   Changes in version 1.13.1                        

• Updates for R_CHECK_LENGTH_1_LOGIC2, R_CHECK_LENGTH_1_CONDITION, classEq.

DEWSeq

             Changes in version 1.1.4 (2020-04-07)                  

• DEWSeq version bump for Bioconductor 3.11

• added missing dependency R.utils

             Changes in version 1.0.2 (2020-02-03)                  
  

• Updated vignette to add htseq-clip pypi links

• LRT tests to results_DEWSeq function

DIAlignR

                   Changes in version 0.99.26                       

• Fixed visualization function.

• Calculating global alignment before iterating over multipeptides.

• Added summary after the alignment.

• Fixed area integrator for missing boundaries.

                   Changes in version 0.99.25                       
  

• Added filePath, Spectra file name, and RunID in one data frame. No need to pass datapath to each function.

• Separate functions to get precursor IDs, OpenSWATH features and chromatogram indices for each precursor across runs.

• Using multi-peptide and updating it in the parent frame.

• Added Alignment rank column.

• Copied C++ code for peak integration from OpenMS.

                   Changes in version 0.99.13                       
  

• Added as.list for S4 objects

                   Changes in version 0.99.12                       
  

• Added boxcar, Gaussian kernel and loess for chromatogram smoothing

• Started documentation for C++ code

• Added support for Microsoft Visual Studio compiler

• Using lists instead of matrix while updating RT and intensities

• Moved python code out of the src directory

                   Changes in version 0.99.11                       
  

• Made changes as suggested in initial review. Updated man/ pages associated with function.

• Link to the file for generating example data is updated.

                   Changes in version 0.99.10                       
  

• Made changes as suggested in initial review. https://github.com/Bioconductor/Contributions/issues/1328#issuecomment-576806498

                   Changes in version 0.99.9                        
  

• Added option to include mz pointer in getOswFiles and getXIC4AlignObj

                   Changes in version 0.99.8                        
  

• Removed R version dependency, have rda files instead of Rdata

                   Changes in version 0.99.7                        
  

• Lowered R version dependency

                   Changes in version 0.99.4                        
  

• Upadted version number

• Corrected tests

• Updated tests to reflect mzR updates, included travis-CI build

• Moved package to Bioconductor

DiffBind

                   Changes in version 2.15.1                        

• Fix issue when extracing SummarizedExperiment from DBA

diffcyt

                    Changes in version 1.7.6                        

• Add ‘show_logFC’ and ‘show_all_cols’ options to ‘topTable’.

DiscoRhythm

             Changes in version 1.3.2 (2020-01-16)                  

• Fixed UI bug preventing job submission under some conditions

distinct

                    Changes in version 1.0.0                        

• Submitted to Bioconductor

dittoSeq

                    Changes in version 1.0.0                        

• Submitted to Bioconductor.

DOSE

                   Changes in version 3.13.2                        

• fixed issue caused by R v4.0.0 (2020-03-12, Thu) - length > 1 in coercion to logical - https://github.com/YuLab-SMU/DOSE/pull/32

                   Changes in version 3.13.1                        
  

• remove S4Vectors dependencies (2019-12-19, Thu) - extend setReadable to support compareClusterResult (2019-12-02, Mon) - add gene2Symbol, keytype and readable slots for compareClusterResult - move compareClusterResult class definition from clusterProfiler (2019-11-01, Fri)

dpeak

             Changes in version 1.0.0 (2020-04-14)                  

• Formatted package for Bioconductor. Changes include:

• Added runnable examples

• Reformatted source code to match Bioconductor practices

DropletUtils

                    Changes in version 1.8.0                        

• Added the downsampleBatches() function for convenient downsampling of batches.

• Preliminary support for using the output of write10xCounts() back in Cellranger.

• Support reading in 10X output files via prefixes in read10xCounts(). Automatic detection of whether a file is Gzipped or not.

• Added chimericDrops() to remove chimeric molecules due to within-sample re-priming.

• Added hashedDrops() to demultiplex cell hashing experiments.

• Added maximumAmbience() to estimate the maximum contribution of the ambient profile.

Dune

             Changes in version 0.9.0 (2019-03-15)                  

• Faster Dune version (from O(nlog(n)) to O(n))

dupRadar

                   Changes in version 1.16.1                        

• Moved project site from Sourceforge to Github.

easyRNASeq

                   Changes in version 2.23.4                        

• Ported changed from 2.22.5

                   Changes in version 2.23.3                        
  

• Ported changed from 2.22.3 & 4

                   Changes in version 2.23.2                        
  

• Ported changed from 2.22.2

                   Changes in version 2.23.1                        
  

• Ported changed from 2.22.1

                   Changes in version 2.22.5                        
  

• Moved the vignette data from the FTP to Git

                   Changes in version 2.22.4                        
  

• Moved the vignette data retrieval to the biocFileCache

                   Changes in version 2.22.3                        
  

• Ensured that misformatted gff3 prefix containing extra white space characters are gracefully handled.

                   Changes in version 2.22.2                        
  

• Fixed a namespace issue

• Extended the cleanup step of the vignette

                   Changes in version 2.22.1                        
  

• Added missing steps to the vignette

• Corrected the RobinsonDelhomme2014 metadata

• Fixed a bug introduced by a dropped functionality in asMates

• Updated package version dependencies

edgeR

                   Changes in version 3.30.0                        

• New function voomLmFit() that combines the limma voom-lmFit pipeline with loss of residual df due to zero counts as for glmQLFit(). The new function is more robust to zero counts than running voom() and lmFit() separately. The new function allows sample quality weights and intra-block correlations to be estimated it incorporates the functionality of duplicateCorrelation() and voomWithQualityWeights() as well.

• New function SE2DGEList() to convert a SummarizedExperiment object into a DGEList object.

• S3 methods for SummarizedExperiment objects are added to the following functions: aveLogCPM(), calcNormFactors(), cpm(), cpmByGroup(), estimateDisp(), filterByExpr(), glmFit(), glmQLFit(), plotMD(), plotMDS(), predFC(), rowsum(), rpkm(), rpkmByGroup() and sumTechReps().

• New cpm and rpkm methods for DGEGLM and DGELRT objects.

• New function effectiveLibSizes() to extract normalized library sizes from an edgeR data object or fitted model object.

• Add as.data.frame methods for DGEExact and DGELRT objects and remove the ‘optional’ argument from as.data.frame.TopTags().

• readBismark2DGE() now forces ‘files’ to be character vector.

• Add warning messages when filterByExpr() is used without specifying group or design.

eisaR

                     Changes in version 1.0                         

• Initial version - R implementation of Exon-Intron Split Analysis (EISA, doi: 10.1038/nbt.3269) - functionality for extracting spliced and unspliced transcript sequences, as well as intron sequences. e.g. for use in RNA velocity analysis

ELMER

                   Changes in version 2.11.0                        

Changes:

• Minor bug fixes to support R 4.0

EnhancedVolcano

                     Changes in version 1.6                         

• removed legendVisible and pLabellingCutoff parameters

• deprecated transcriptPointSize, transcriptLabSize, transcriptLabCol, transcriptLabFace, transcriptLabhjust, transcriptLabvjust, boxedlabels, and drawconnectors parameters

• now pad xlim by +/- 1

• moved default position of labels to be central to its respective point

• added ‘colGradient’, which colours points continuously based on p-value

EnMCB

                   Changes in version 0.99.12                       

NEW FEATURES

• Update vignettes.

SIGNIFICANT USER-VISIBLE CHANGES

• Delete unused data.

BUG FIXES

• Some fixes related to test functions.

ENmix

                   Changes in version 1.22.6                        

• add function: combp,ipdmr,mhtplot,p.qqplot

                   Changes in version 1.22.2                        
  

• removed function bmiq.mc and ComBat.mc

EnrichmentBrowser

                   Changes in version 2.18.0                        

• Gene sets: supporting additional gene set databases - getGenesets(db = “msigdb”) to obtain gene sets from the MSigDB for 11 different species (via msigdbr) - getGenesets(db = “enrichr”) to obtain gene set libraries from Enrichr for 5 different species

• Gene ID mapping for gene sets and gene regulatory networks (function idMap)

• Implementation of a variance-stabilizing transformation for RNA-seq data (function normalize with argument norm.method = "vst") to simplify the application of legacy enrichment methods

enrichplot

                    Changes in version 1.7.3                        

• update cnetplot color scale to tolerate with skewed foldchange (2020-03-13, Fri) - https://github.com/YuLab-SMU/enrichplot/pull/40

                    Changes in version 1.7.1                        
  

• cnetplot for compareClusterResult (compareCluster output) (2019-12-02, Mon) - move barplot, dotplot and fortify methods of compareClusterResult from clusterProfiler (2019-11-2, Sat)

ensembldb

                   Changes in version 2.11.1                        

• Fix mapIds issue.

• Add gc_count to the transcripts table.

• Ensure mapIds returns a result equal to the number of input keys - even if none of them could be mapped (issue #104).

ensemblVEP

                   Changes in version 1.30.0                        

• add support for Ensembl release 99

EpiTxDb

             Changes in version 0.99.0 (2020-02-25)                 

• Submitted to Bioconductor

epivizrServer

                   Changes in version 999.999                       

• This NEWS file is only a placeholder. The version 999.999 does not really exist. Please read the NEWS on Github: <URL: https://github.com/epiviz/epivizrServer>

ERSSA

                    Changes in version 1.5.1                        

• Better implementation of jitter plot in ggplot2_dotplot

• plot_marginalPlot set to plot median as default, previously set to plot mean

evaluomeR

             Changes in version 1.3.41 (2019-01-07)                 

• Minor bug fix for R 4.0 devel.

             Changes in version 1.3.4 (2019-12-19)                  
  

• Adding ‘plotMetricsClusterComparison’ method.

             Changes in version 1.3.3 (2019-12-16)                  
  

• Refactoring ‘getOptimalKValue’ method

• Adding stabilitySet and qualitySet

             Changes in version 1.3.2 (2019-11-12)                  
  

• Added new methods: Dependency with FPC added. Stability/stabilityRange also outputs cluster information like centers.

             Changes in version 1.3.0 (2019-11-12)                  
  

• Added new methods: plotMetricsMinMax, plotMetricsBoxplot, plotMetricsCluster, plotMetricsCluster and plotMetricsViolin

exomePeak2

            Changes in version 0.99.92 (2020-03-10)                 

• Fix several issues commented by the bioconductor reviewer

ExperimentHub

                   Changes in version 1.13.0                        

NEW FEATURES

• (1.13.5) New function removeResources for removing locally downloaded cached resources. Nicer interface than using cache. Improved documentation on use of setting a cache to NULL to also remove resources.

• (1.13.4) Adds option ask to constructor. Default: True. Ask will ask user to create default ExperimentHub location and if in an non interactive session utilize a temporary directory. If False, the default directory is created and utilized without prompting.

BUG FIXES

• (1.13.8) Updated has_internet to nslookup. Certain locations block has_internet from running (block google dns). switched so can query the hub directly

• (1.13.7) Fixed messages to be more informative

• (1.13.2) Aaron’s corrections to setExperimentHubOptions.

USER-VISIBLE CHANGES

• (1.13.1) Match ERROR message when resource not found in database. Instead of a generic “unknown key” give more detailed information. This is consistent with AnnotationHub/Hub-classes. If resource hasn’t been completely removed from database, gives when the resource was removed. If the resource is available but after the snapshot date being utilized, specialized message.

ExperimentHubData

                   Changes in version 1.13.0                        

MODIFICATIONS

• 1.13.1 add check for valid Title and Description in metadata file. It should not be empty or NA

ExploreModelMatrix

                   Changes in version 0.99.0                        

• Prepared for Bioconductor submission

                    Changes in version 0.2.0                        
  

• Added pseudoinverse, variance inflation factor, coefficient correlation and co-occurrence plots. - Arguments flipCoord, textSize, textSizeLabs, lineWidth, addColor and colorPalette in VisualizeDesign have been renamed (adding Fitted as a suffix) to allow corresponding arguments for other types of plots.

                    Changes in version 0.1.0                        
  

• Initial version

fcoex

             Changes in version 1.1.1 (2020-05-08)                  

• Updated fcoex example object “fc”.

fgsea

                   Changes in version 1.13.4                        

• mapIdsList for faster conversion of leadingEdges

• experimental support of hypergeometric tests with fora() and collapsePathwaysORA()

                   Changes in version 1.13.3                        
  

• experimental support for one-tailed tests

                   Changes in version 1.13.2                        
  

• fgsea() implementation changed from simple to multilevel algorithm

• proper handling of duplicate genes in gene sets for fgseaSimple() and fgseaMultilevel()

fishpond

                    Changes in version 1.4.0                        

• Added isoformProportions(), which can be run after scaleInfReps() and optionally after filtering out transcripts using labelKeep(). Running swish() after isoformProportions() will produce differential transcript usage (DTU) results, instead of differential transcript expression (DTE) results. Example in vignette. + Default number of permutations increased from 30 to 100. It was observed that there was too much fluctuation in the DE called set for nperms=30 across different seeds, and setting to 100 helped to stabilize results across seeds, without increasing running time too much. For further reduced dependence on the seed, even higher values of nperms (e.g. 200, 300) can be used.

                    Changes in version 1.3.8                        
  

• Added isoformProportions(), which can be run after scaleInfReps() and optionally after filtering out transcripts using labelKeep(). Running swish() after isoformProportions() will produce differential transcript usage (DTU) results, instead of differential transcript expression (DTE) results. Example in vignette.

                    Changes in version 1.3.4                        
  

• Default number of permutations increased from 30 to 100. It was observed that there was too much fluctuation in the DE called set for nperms=30 across different seeds, and setting to 100 helped to stabilize results across seeds, without increasing running time too much. For further reduced dependence on the seed, even higher values of nperms (e.g. 200, 300) can be used.

flowCore

                    Changes in version 2.0.0                        

• keyword<- behaves now as normal replacement method, i.e. keyword(fr) <- list(name = value) will replace the entire keyword list instead of partial updating/inserting, to achieve latter, use keyword(fr)[“name”] <- value - [ method (e.g. fr[, 1:4]) no longer deletes $PnX keywords automatically so that it is compatible with cytoframe

                    Changes in version 1.53                         
  

• ‘workFlow’ class and related classes and methods now defunct #148 – superseded by flowWorkspace - Add support for multiple data segments in ‘read.FCSheader’ - Fixed some edge cases with ‘read.FCS ‘with column.pattern argument #157 - Added ‘transform_gate’ methods for geometric transformations of gates - Added ‘collapse_desc’ for coercing keyword lists in to character - ‘spillover’ method for calculating compensation matrix from a ‘flowSet’ of controls moved to ‘flowStats’ - Added ‘filter_keywords’ for filtering lists of keywords
• Deprecate description and description<- for keyword and keyword<- to reduce redundancy and give consistent behavior for cytoframe RGLab/flowWorkspace #311

flowSpecs

             Changes in version 1.1.4 (2020-04-27)                  

• Chaning usage from flowCore::Description to flowCOre::keyword due to deprecation.

             Changes in version 1.1.3 (2020-04-21)                  
  

• Adding an outlier removal step in the internal peakIdenti function

• Removing .internal calls in anticipation of the R 4.0 deprecation

• Minor bug fixes in internal fucntions.

             Changes in version 1.1.2 (2020-01-27)                  
  

• bug fix enabling multiple FSC measurements when generating the unmix matrix

             Changes in version 1.1.1 (2019-11-28)                  
  

• bug fix enabling multiple SSC measurements when generating the unmix matrix

flowSpy

             Changes in version 1.1.5 (2020-04-20)                  

• Fixed installation errors in Linux and Windows

• Fixed legend name of figure

• Fixed errors in building vignette

             Changes in version 1.0.4 (2020-03-19)                  
  

• Fixed installation errors in Linux and Windows

             Changes in version 1.0.3 (2020-03-17)                  
  

• Fixed bugs in runDiff

             Changes in version 1.0.1 (2020-02-15)                  
  

• Add uniform downsampling in function processingCluster

• Fixed some warnings in the checking process of Bioc 3.10

FoldGO

             Changes in version 1.5.2 (2020-04-23)                  

• Not fold-change-specific bars removed from plots

• Citation file added

             Changes in version 1.5.1 (2020-04-21)                  
  

• issue with incompatible regex for inst/extdata directory fixed

• R version dependency switched to 4.0

FRASER

                   Changes in version 0.99.1                        

• Introduction of the shinyApp

                   Changes in version 0.99.0                        
  

• This is the initial setup of the FRASER package.

• Use SummarizedExperiment as superclass

• Integrate package into the Bioconductor infrastructure

GAPGOM

             Changes in version 1.3.1 (2020-04-10)                  

Changed

• Author name in Readme, DESCRIPTION and LICENSE

• Copyright year 2018 -> 2020

Fixed

• test_parsing.R to work with latest Bioc (3.11)

• R depends version for Bioc 3.11

GARS

                    Changes in version 1.8.0                        

• bug fixed and publication added

GateFinder

                    Changes in version 1.7.1                        

• changed conditional check on class to be consistent with R 4.0.0 for Bioconductor 3.11 release

gCMAP

                   Changes in version 1.31.1                        

• CHANGE: The gCMAP and gCMAPWeb packages are deprecated and will be removed from Bioconductor version 3.12.

gCMAPWeb

                   Changes in version 1.27.1                        

• CHANGE: The gCMAP and gCMAPWeb packages are deprecated and will be removed from Bioconductor version 3.12.

gCrisprTools

Version: 1.15.0 Category: Various code updates, new functions added for visualization, compatibility with modern R objects. Russell Bainer redesignated as official maintainer. Text:

gdsfmt

                   Changes in version 1.24.0                        

NEW FEATURES

• new option ‘allow.error’ in openfn.gds() for data recovery

• new option ‘log.only’ in diagnosis.gds()

• new C functions GDS_Node_Unload() and GDS_Node_Load() in R_GDS.h

• new sparse array data types in GDS (SparseReal32, SparseReal64, SparseInt8, SparseInt16, SparseInt32, SparseInt64, SparseUInt8, SparseUInt16, SparseUInt32, SparseUInt64)

• the opened gds file will be closed when the object is garbage collected

UTILITIES

• zlib updated to v1.2.11 from v1.2.8

• xz updated to v5.2.4 from v5.2.3

• LZ4 updated to v1.9.2 from v1.7.5

• showfile.gds() does not return the object of ‘gds.class’

• new ‘n’ and ‘depth’ in print.gdsn.class() and print.gds.class()

GeneNetworkBuilder

                   Changes in version 1.29.1                        

• Add BiocStyle and magick into Suggests

GeneSelectMMD

                   Changes in version 2.31.2                        

• reformat NEWS file

                   Changes in version 2.31.1                        
  

• update DESCRIPTION: maintainer’s email address; exclude ‘Biobase’ and ‘survival’ from “Imports”

• update NAMESPACE: add “Import(Biobase)”

• fixed a bug in trans.R: the ‘diff’ in “tmp > 1 || diff < eps” is a vector

• revised visual.R: shorten strings in ‘mytitle’

• change Weiliang’s email address in all .Rd files

• revised plotHistDensity.Rd: shorten strings in ‘mytitle’

GENESIS

                   Changes in version 2.17.4                        

• Fix a bug that prevented use of multiple environment variables in GxE.

                   Changes in version 2.17.3                        
  

• Allow divergence to be NULL in pcair and pcairPartition.

                   Changes in version 2.17.1                        
  

• Fix a bug in null model when starting variance component is close to 0.

geNetClassifier

                   Changes in version 1.27.1                        

• Minor update for R 4.0.

GeneTonic

                   Changes in version 0.99.0                        

Other notes

• GeneTonic is now submitted to Bioconductor!

                   Changes in version 0.10.0                        
  

New features

• The functions for comparing different res_enrich, namely gs_radar, gs_summary_overview_pair, and gs_horizon were internally rewritten to accept correctly the comparison elements - The vignette now covers completely the usage cases, with the full description of the user interface of GeneTonic - The introductory tours are available for all the main panels of GeneTonic. Feel free to try them out!

Other notes

• Some widgets have been added in the UI of GeneTonic to enable finer control of the output aspect - Examples and unit tests have been further expanded, with better messages for checking progress - check_colors verify that color palettes are correctly provided - Info on GeneTonic is now provided with modal dialog windows, rather than in a separate tab - The tab names in the main app were slightly edited to better describe their content - The info boxes are now shown with a uniform style, based on the bs4Card UI element - The UI elements have now a better spacing throughout the different tabs - Soon the package will be submitted to Bioconductor!

                    Changes in version 0.9.0                        
  

New features

• GeneTonic sports a blazing new hex sticker - say bye to the original draft! - The overview DT datatables has some styling with color bars - e.g. for DE results - to enhance the visual perception of numeric values (e.g. log2FoldChange) - gs_heatmap can now take a custom list of gene identifiers (when no geneset is passed) - The color palettes in enrichment maps now respect the values and the range specified of the numeric values to be used for mapping to colors - gs_mds is now optionally returning a data.frame, to be further used for custom plotting or downstream processing - gs_summary_overview now has coloring enabled by the variable of choice

Other notes

• The UI has received some restyling (e.g. in the choice of the icons for the dropdown menus, or the name of some buttons) - Added tour contents for most of the functionality - Added link to the demo instance - Added examples for overlap functions, gene info buttons, map2color, and deseqresult2df - Extended documentation of some parameters - Some functions have gained an alias for calling them: gs_spider is equivalent to gs_radar, and gs_sankey is equivalent to gs_alluvial

                    Changes in version 0.8.0                        
  

New features

• GeneTonic now delivers bundled example objects to make examples and tests slim - gs_volcano can now plot points by different colors according to the columns of interest - GeneTonic has a fully fledged manual describing its functionality and user interface

Other notes

• Now using ids for genes and genesets for exchanging information in the app - Added examples for all functions - Most tabs have working tours - anchor and text elements

                    Changes in version 0.7.0                        
  

New features

• Introduced a uniform interface for calculating different similarity/distance matrices. This enables the usage in the different functions that might need such matrices for further downstream processing (e.g. enrichment_map(), gs_mds()) - First appearance of gs_dendro() to display distance matrices with some visualization sugar, as an alternative to other methods - The n_gs and gs_ids are exposed to more functions to enable custom subsets of the enrichment results to be inspected

                    Changes in version 0.6.0                        
  

New features

• gs_heatmap now relies on ComplexHeatmap, to avoid the issues with Shiny of not displaying the outputs in the app, and enabling a comfortable heatmap annotation - Many functions gain the possibility to pass a set of custom geneset identifiers to be added to the top N sets (default): among these, gs_mds, gs_volcano (parameter: gs_labels), gs_alluvial, ggs_network, enrichment_map, and enhance_table (using gs_ids)

Other notes

• gs_ggheatmap got renamed to gs_scoresheat - The report generated from the bookmarked content is expanded in its default content

                    Changes in version 0.5.0                        
  

New features

• GeneTonic now enforces a format for res_enrich, and provides some conversion functions, shake_*(). Requirements are specified in the documentation, if an appropriate converter does not (yet) exist. - The reporting feature is active to some extent on the bookmarked content.

                    Changes in version 0.4.0                        
  

New features

• Added functionality for bookmarking - Bookmarking can work (PoP) by pressing a key (left control)! - gene_plot can enforce a plot type overriding the default based on the number of samples per condition - GeneTonic uses now bs4Dash and many of its nice features, replacing the previous implementation based on shinydashboard

                    Changes in version 0.3.0                        
  

Other notes

• Rearranging the order of parameters to harmonize it across functions, and uniforming similarly called parameters

                    Changes in version 0.2.0                        
  

New features

• added geneset scoring calculation and corresponding heatmap

                    Changes in version 0.1.0                        
  

New features

• much of the functionality available, in a proof of concept format

                    Changes in version 0.0.1                        
  

New features

• backbone of the project started!

GenomeInfoDb

                   Changes in version 1.24.0                        

NEW FEATURES

• Add getChromInfoFromUCSC(), getChromInfoFromNCBI(), and getChromInfoFromEnsembl().

DEPRECATED AND DEFUNCT

• Deprecate fetchExtendedChromInfoFromUCSC() in favor of getChromInfoFromUCSC().

GenomicDataCommons

                   Changes in version 1.11.1                        

• add support for fetching field descriptions

GenomicFeatures

                   Changes in version 1.40.0                        

NEW FEATURES

• Small improvements to makeTxDbFromEnsembl(): - check validity of user supplied transcript attribute code - report nb of fetched transcripts and genes during progress - produced TxDb will “remember” which transcript attribute code was used

SIGNIFICANT USER-VISIBLE CHANGES

• genes() now prints a message when genes are dropped.

• getChromInfoFromUCSC() is now defined in the GenomeInfoDb package. Note that the new function is a much improved version of the old one but also the returned data frame has its columns named differently! See ?getChromInfoFromUCSC in the GenomeInfoDb package for the details.

• Argument ‘goldenPath_url’ was renamed ‘goldenPath.url’ in functions makeTxDbFromUCSC(), makeFeatureDbFromUCSC(), makeTxDbPackageFromUCSC(), and makeFDbPackageFromUCSC().

• Default value for argument ‘circ_seqs’ was changed from DEFAULT_CIRC_SEQS to NULL in all functions that have this argument.

• Global constant DEFAULT_CIRC_SEQS (character vector) was removed. It is now defined in GenomeInfoDb but no longer exported, at least for now.

BUG FIXES

• Make asGFF() method for TxDb objects robust to absence of CDS ranges.

GenomicRanges

                   Changes in version 1.40.0                        

NEW FEATURES

• Add trim() method for GRangesList objects.

GenomicScores

                    Changes in version 2.0.0                        

USER VISIBLE CHANGES

• Added a shiny app available through the function ‘igscores()’.

• Added support for genomic score packages (e.g., MafH5.*) that use HFD5 files as a backend.

• Added a new function ‘rgscores()’ for randomly sampling genomic scores.

GEOquery

                   Changes in version 2.55.1                        

Bug fixes:

• Fix test failure due to stricter boolean check lengths [#568ae94fb95, from @russHyde]

• Fix failure on empty file [#88741521a0e, from @vlakam]

GGPA

            Changes in version 0.99.10 (2020-04-14)                 

• Formatted package for Bioconductor. Changes include:

• Added runnable examples

• Reformatted source code to match Bioconductor practices

                    Changes in version 0.9.6                        
  

• Made the following significant changes

• The vignette was updated by incorporating the illustration of the workflow to download the prior disease graph from the companion website (http://www.chunglab.io/ddnet).

• plot(): Improve visualization, e.g., using a circle mode.

                    Changes in version 0.9.5                        
  

• Made the following significant changes

• GGPA(): Allow to incorporate a prior phenotype graph.

• plot(): Use GGally (ggnet2) instead of Rgraphviz for the phenotype graph visualization.

                    Changes in version 0.9.1                        
  

• The first version of GGPA R package.

ggtree

                    Changes in version 2.1.6                        

• Now geom_tiplab() works with unrooted layouts (ape, equal_angle and daylight) (2020-04-23, Thu) - https://github.com/YuLab-SMU/ggtree/issues/292 - bug fixed of layoutEqualAngle (2020-04-09, Thu) - in tibble v=3.0.0, df$x = NA will store df$x as lgl variable and assign numeric value to df$x will throw error. Now change to df$x = 0 in layoutEqualAngle.

                    Changes in version 2.1.5                        
  

• bug fixed of calculating inset width and height - https://github.com/YuLab-SMU/ggtree/issues/289

                    Changes in version 2.1.4                        
  

• import aplot::xrange

                    Changes in version 2.1.3                        
  

• move xlim2 and ylim2 to aplot package (2020-03-30, Mon) - https://cran.r-project.org/package=aplot - remove mutate_ as it was deprecated in dplyr (2020-03-25, Wed) - fixed mutate bug caused by new version of dplyr and tidytree in daylight layout (2020-03-16, Mon) - https://github.com/YuLab-SMU/ggtree/issues/282

                    Changes in version 2.1.2                        
  

• expand_scale was deprecated in ggplot2 v=3.3.0, import expansion instead (2020-03-12, Thu) - bug fixed of determined layout for ggplot(tree) + geom_tiplab() (2020-01-26, Sun) - https://github.com/YuLab-SMU/ggtree/issues/272 - set unrooted layout to use coord_fixed by default (2020-01-25, Sat) - if layout = “ape”, use ape unrooted layout - https://github.com/YuLab-SMU/ggtree/pull/273

                    Changes in version 2.1.1                        
  

• export geom_highlight as an alias of geom_hilight (2020-01-08, Wed)
• set clip=”off” for all layouts (2019-12-06, Fri) - not passing fontface if geom is image or phylopic in geom_tiplab and geom_nodelab (2019-11-29, Fri) - import and re-export guide_legend, scale_colour_manual, scale_color_manual, scale_fill_manual and margin from ggplot2 - offspring method for ggtree object (2019-11-21, Thu) - fixed revts to work with collapse (2019-11-18, Mon) - convert roxygen documents using markdown (2019-11-01, Fri) - extend xlim2 and ylim2 to support discrete scale. - xlim2 and ylim2 to uniformize axis limits of ggplot objects (2019-10-31, Thu) - https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot - https://yulab-smu.github.io/treedata-book/docs/chapter10.html#axis_align
• fixed fontface warning message when align=TRUE in geom_tiplab (2019-10-30, Wed) - https://github.com/YuLab-SMU/ggtree/issues/260

gmoviz

                   Changes in version 0.99.8                        

• Submitted to Bioconductor

GNET2

                    Changes in version 1.3.7                        

• The retuun of extract_edges() now contains the group score.

                    Changes in version 1.3.3                        
  

• Add function to extract the network from the gnet result

                    Changes in version 1.3.2                        
  

• Fix plot order issue.

• Add group split procedure for module groups with too many genes.

                    Changes in version 1.3.1                        
  

• Fix the initial group number limit.

GOfuncR

                    Changes in version 1.7.1                        

USER-LEVEL CHANGES

• update GO-graph (version 23-Mar-2020)

GOSemSim

                   Changes in version 2.13.1                        

• add new citation (2020-03-19, Thu) - fixed compiling error due to the change of Rcpp - https://github.com/YuLab-SMU/GOSemSim/issues/27

GPA

                    Changes in version 1.1.0                        

• Made the following significant changes

• Incorporate ShinyGPA developed by Emma Kortemeier as a part of the R package.

• Add fitAll() to fit GPA models for possible pairs of phenotypes.

• Add shinyGPA() to open the shiny app for the interactive pleiotropy visualization.

             Changes in version 0.99.9 (2020-04-14)                 
  

• Formatted package for Bioconductor. Changes include:

• Added runnable examples

• Reformatted source code to match Bioconductor practices

                    Changes in version 0.9.3                        
  

• Made the following significant changes

• Incorporate R package vignette.

• assoc(), fdr(): allows association mapping & local FDR for specific association status.

• aTest(), pTest(): message() was replaced with cat().

                    Changes in version 0.9.2                        
  

• Made the following significant changes

• Add se() to provide parameter estimates and their standard errors.

                    Changes in version 0.9.1                        
  

• Made the following significant changes

• Add fdr() to provide local FDR that a SNP is not associated with each phenotype.

• Add assoc() for association mapping.

• The function aTest() and methods show() and cov() for class ‘GPA’ now provide estimates and standard error for the ratio of q in each association class over the baseline.

• In GPA(), ‘initBetaMean’ argument is replaced with ‘initBetaAlpha’.

• Generally improve robustness of functions by checking input for arguments.

                    Changes in version 0.9.0                        
  

• The first version of GPA R package.

graphite

             Changes in version 1.33.1 (2020-10-24)                 

• Updated all pathway data.

gscreend

                    Changes in version 1.0.1                        

• The data input function raises errors, when column naming concerning sgRNAs or genes in not clear.

• Functions that can only be run after analysing data raise errors when you try to run them before the model has been fitted and statistics computed.

GSEABenchmarkeR

                    Changes in version 1.8.0                        

• Extended support for benchmarking user-defined inputs: - mixing of pre-defined and user-defined enrichment methods (functions runEA and evalTypeIError) - simplified passing on of additional arguments to user-defined enrichment methods for functions runEA and evalTypeIError

• The TCGA RNA-seq compendium can now also be obtained via curatedTCGAData using loadEData("tcga", mode = "cTD")

GSVA

                    Changes in version 1.36                         

USER VISIBLE CHANGES

• Improved management of parallel calculations by using the BiocParallel package. This facilitates calculating GSVA scores from gene expression data matrices with thousands of samples. See arguments ‘parallel.sz’ and ‘BPPARAM’ in the manual page of the ‘gsva()’ function.

• Improved implementation of the SSGSEA method (‘method=”ssgsea” in the call to ‘gsva()’) that makes calculations with this option about one order of magnitude faster. Improvement thanks to Alexey Sergushichev (https://github.com/rcastelo/GSVA/pull/15).

• The function ‘gsva()’ now issues a warning when one or more gene sets are singletons, i.e., they are formed by just one feature/gene.

Gviz

                   Changes in version 1.32.0                        

NEW FEATURES

• Exposed the possibility to specify centromere shape

• AlignmentsTracks can visualize “indels”

• SequenceTrack has new subclass: SequenceRNAStringSetTrack

• added RNASequenceTrack

BUG FIXES

• Fixed issue in .buildRange (internal) to correctly build package on windows

Harman

                   Changes in version 1.15.0                        

• Previously, if no random seed is specified to the harman function, a seed of 0 was used. Now a random seed between 0 and 1e9 is picked at random.

HDF5Array

                   Changes in version 1.16.0                        

NEW FEATURES

• New h5writeDimnames()/h5readDimnames() functions for writing/reading the dimnames of an HDF5 dataset to/from the HDF5 file. See ?h5writeDimnames for more information.

• Add full support for HDF5Array objects of type “raw”: - writeHDF5Array() now works on a DelayedArray object of type “raw” (it creates an H5 dataset of type H5T_STD_U8LE). - The HDF5Array() constructor now should return an HDF5Array object of type “raw” when pointed to an H5 dataset with an 8-bit width type (e.g. H5T_STD_U8LE, H5T_STD_U8BE, H5T_STD_I8LE, H5T_STD_I8BE, H5T_STD_B8LE, H5T_STD_B8BE, etc…)

• Add ‘H5type’ argument to writeHDF5Array().

• h5mread() now supports contiguous (i.e. unchunked) string data.

SIGNIFICANT USER-VISIBLE CHANGES

• HDF5Array objects now find their dimnames in the HDF5 file. writeHDF5Array() and as(x, “HDF5Array”) know how to write the dimnames to the HDF5 file, and the HDF5Array() constructor knows how to find them. See ?writeHDF5Array for more information.

BUG FIXES

• Fix bug causing character data to be truncated when written to HDF5 file.

• Fix h5mread() inefficiency when the user selection covers full chunks.

• h5mread() now handles character NAs consistently with rhdf5::h5read().

• Fix writeHDF5Array() error on character array filled with NAs.

HIPPO

             Changes in version 0.99.3 (2020-03-25)                 

• Submitted to Bioconductor

HPAanalyze

                     Changes in version 1.5                         

• Changes in version 1.5.3

  • Update built-in data to HPA version 19.

• Changes in version 1.5.2

  • Minor bug fixes.

• Changes in version 1.5.1

  • Add documentation with pkgdown. Minor updates to documentation.
  • tidyr and readr dependencies have been replaced with base R solutions.
  • Importing data from hpar is no longer supported.
  • hpaDownload function was updated to correctly download data in HPA version 19.

• Changes in version 1.5.0

  • Starting devel for Bioconductor 3.10

hpar

                    Changes in version 1.29                         

Changes in version 1.29.1

• Update email address <2020-03-29 Sun>

HTSeqGenie

                   Changes in version 4.17.1                        

• fix bug in targetLenght plotting in reportSummaryQC

• make countGenomicFeatuers work with subclasses of GRangesList

hypeR

                   Changes in version 1.3.00                        

• Force version bump for bioconductor release 3.10

ideal

                   Changes in version 1.12.0                        

New features

• Implemented a series of gentle fail mechanisms to avoid abrupt crashing of the app if the expected objects or formats are not provided

Other notes

• Alignments of UI elements have been adjusted - Updated citation info - the preprint for ideal, “ideal: an R/Bioconductor package for Interactive Differential Expression Analysis”, is now published at bioRxiv, https://doi.org/10.1101/2020.01.10.901652

idr2d

                    Changes in version 1.0.4                        

• changed max_gap default value from 0 to -1 to conform with convention

• updated reference to IDR2D publication

                    Changes in version 1.0.3                        
  

• added option to disable jitter

• added min_value and max_value parameters to estimate_idr2d_hic

• fix block size display for draw_hic_contact_map

                    Changes in version 1.0.2                        
  

• added parser for HiC-Pro contact maps (.matrix and .bed files)

• added function to visualize contact maps, showing only reproducible blocks

                    Changes in version 1.0.1                        
  

• fixed alpha level in rank and value scatterplots

• bold font face for axis and legend titles

IgGeneUsage

             Changes in version 1.1.6 (2020-04-01)                  

• Corresponding methodology published in Bioinformatics

• Speedup in posterior prediction

immunoClust

                   Changes in version 1.19.4                        

• CHANGES * code cleaning

                   Changes in version 1.19.3                        
  

• CHANGES * fixes a compiler error under windows

                   Changes in version 1.19.1                        
  

• CHANGES * bugfix in transformParam.immunoMeta

infercnv

             Changes in version 1.3.6 (2020-03-20)                  

• Fix a read.table() call who’s behavior was changed by the latest R base devel changes.

             Changes in version 1.3.5 (2020-03-02)                  
  

• Fix saving file name for preliminary object.

• Added an option to plot_cnv(), plot_chr_scale, that allows to plot chromosomes proportionally to their full size. Either a list of chromosomes sizes is provided, or the last gene stop position + 10k bp is assumed. Gene width is proportional to the area in the chromosomes they “cover” (midpoints between genes). This option is slower than the default as rasterization can not be applied when drawing the heatmap.

             Changes in version 1.3.4 (2020-02-18)                  
  

• Added options to save rds results after each step (save_rds) or final results (save_final_rds), with default TRUE.

• Fix size of pdf output settings to use the given width and height values instead of the “USr” format.

• Fixes in plot_cnv() when using observation groups with 1 or 2 cells.

• Fix checks in plot_cnv() of references for when subclusters are not defined in the object.

• Fix (sub)cluster definition when an annotation only has 1 cell (although this should probably be avoided).

             Changes in version 1.3.3 (2020-02-07)                  
  

• Large speed improvements in plot_cnv() that are more significant the bigger the matrix size.

• plot_cnv() now uses clustering information stored in the infercnv object for the references instead of rerunning the clustering every time.

• Fix assumption that length(class(obj)) == 1, in this case for matrix objects for R 2020-01-28 update.

• Made color.palette an exported function so that it can be used for the “custom_color_pal” option.

• Updated some logging to be more accurate.

             Changes in version 1.3.2 (2019-12-06)                  
  

• Added an new option “custom_color_pal” to plot_cnv() so a user can provide their choice of colors for the heatmap.

             Changes in version 1.2.2 (2019-12-06)                  
  

• Fixed check of how HMM results are reported by so that add_to_seurat works when HMM_report_by is “cell” but HMM analysis_mode was “subclusters”.

• Fix check of HMM_report_by setting in add_to_seurat when the option was not specified.

             Changes in version 1.2.1 (2019-11-14)                  
  

• Fix R_CHECK_LENGTH_1_LOGIC2 related error because an argument was checked before matching to it’s list of potential arguments.

• Fix text outputs for CNV reports when running with report_by=”cell”.

• Fix add_to_seurat method to handle CNVs reported by cells in HMM predictions.

• Fix how options used for a run are stored in the object and compared when trying to reload previous results so that it handles arguments given as variables in the call to run(). This also fixes the command-line script to run infercnv.

InPAS

                   Changes in version 1.19.1                        

• replace all class by is.

INSPEcT

                   Changes in version 1.16.1                        

• added the slot ‘version’ that store the version used in each object created (IMPORTANT! objects without this slot, i.e. created before this version cannot be used anymore and must be regenerated)

• added 2 wrap-up function to run the entire INSPEcT pipeline with a single command line

• ratePvals modified (calculated at the time of modeling via calculateRatePvals method and stored into slot ratePvals of the class INSPEcT)

• changes in model params accession (modeling parameters are set via modelRates and only accessed via modelingParams; model selection parameters are set via calculatePvals and only accessed via modeingParams)

• modifications to INSPEcT-GUI (Added Fix-Y-Axis & pvals in Y-labels, Confidence intervals controlled by a button rather than the checkbox)

• converted gene class names from a,c,b for synthesis, processing and degradation to s,p,d

intansv

                   Changes in version 1.29.0                        

Notes

• Fix build error on Windows and Mac.

IntEREst

                   Changes in version 1.12.0                        

BUG FIXES

• Replacing class( x ) == “foo” with is( x , “foo”) .

IRanges

                   Changes in version 2.22.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Resync with change to smoothEnds() in R 4.0. In R 4.0, stats::smoothEnds() always returns an integer vector when the input is an integer vector. smoothEnds() on an IntegerList now reflects this: it returns an IntegerList object instead of a NumericList object.

DEPRECATED AND DEFUNCT

• RangedData objects are now defunct. RangedData objects are defunct in BioC 3.11. They were deprecated in BioC 3.9 and, before that, their used has been discouraged in favor of GRanges or GRangesList objects since BioC 2.12, that is, since 2014.

BUG FIXES

• Fix restrict() method for RangesList objects for when ranges are dropped.

iSEE

                   Changes in version 1.99.9                        

• Fixed slot names in the ReducedDimensionPlot() man page.

                   Changes in version 1.99.8                        
  

• Protect against transient invalid selected index; fixes #400. - Forced renderDT to rerun expression upon panel reorg.

                   Changes in version 1.99.7                        
  

• Fixed out-of-date vignette content.

                   Changes in version 1.99.6                        
  

• Added static screenshots to vignettes. - Added GitHub Actions for continuous integration and deployment. - Updated Docker base image to bioconductor/bioconductor_docker:devel.

                   Changes in version 1.99.5                        
  

• Export utilities relevant to downstream panel development.

                   Changes in version 1.99.4                        
  

• Added options for dynamic choice of single/multiple selection sources. - Fixed bug around NA groupings in subsetPointsByGrid(). - Explicitly notify the user when removing invalid panels supplied by a landing page.

                   Changes in version 1.99.3                        
  

• Fixed occurences of rowData in RowDotPlot panels. - Refactored .create_visual_box(). - Refactored visual parameter sections into generics. - Apply global option selected.color to single selections.

• Added panel.width, panel.height, and assay to global options. - Added .checkboxInputHidden().

                   Changes in version 1.99.2                        
  

• Added extension points to the API. - Added global settings using iSEEOptions. - Added .allowableYAxisChoices() and .allowableXAxisChoices() methods to intercept choices of x/y-axis variables.

                   Changes in version 1.99.1                        
  

• Allowed customization of landing pages (from calling iSEE() in no-SE mode) for enterprise deployments. - Allowed export of plot and table panel outputs as PDF and CSV files, respectively. - Fixed handling of se objects missing dimnames. - Added createCustomPlot() and createCustomTable() to provide on-ramp for making customized panels. - Allowed global setting using iSEEOptions. - Expanded class and slot names from “Feat” to “Feature”, “Samp” to “Sample”, “RedDimPlot” to “ReducedDimensionPlot”. - Renamed “StatTable” to “DataTable”.

                   Changes in version 1.99.0                        
  

• Refactored panel implementation as S4 classes. - Display a spinner while panels are rerendering. - Refactored heatmap panel to use ComplexHeatmap.

                    Changes in version 1.7.2                        
  

• Added notification on birthday. - Enabled hiding of the *DataPlot UI elements.

                    Changes in version 1.7.1                        
  

• Fix rbind() of data.frame and DataFrame objects. - Fix error related to using && with variable length greater than 1. - Replace deprecated scater argument. - Replace deprecated functions: SingleCellExperiment::clearSpikes(), SingleCellExperiment::clearSizeFactors().

                    Changes in version 1.7.0                        
  

• Bioconductor release.

iSEEu

                   Changes in version 0.99.8                        

• Trigger new build on the single package builder.

                   Changes in version 0.99.7                        
  

• Replace !=”” by nzchar(). - Use 4-space indent. - Add info on how to contribute to iSEEu, including coding style.

                   Changes in version 0.99.6                        
  

• Trigger new build on the single package builder.

                   Changes in version 0.99.5                        
  

• Add more suggested packages. - Add screenshot images to the vignette. - More realistic examples in the vignette. - Fix GeneSetTable to acknowledge initial value of “Selected”.

                   Changes in version 0.99.4                        
  

• Fix to GitHub action R-CMD-check.

                   Changes in version 0.99.3                        
  

• Set up GitHub action R-CMD-check. - Remove Travis CI covr code coverage and pkgdown site deployment. - Fix man page warning.

                   Changes in version 0.99.2                        
  

• Create observer for “Assay” in DiffStatTable. - Update NEWS.

                   Changes in version 0.99.1                        
  

• Trigger new build on the single package builder.

                   Changes in version 0.99.0                        
  

• Added panel DifferentialStatisticsTable. - Added panel DynamicReducedDimensionPlot. - Added panel GeneSetTable. - Added panel MAPlot. - Added panel ReducedDimensionHexPlot. - Added panel VolcanoPlot. - Added mode modeEmpty. - Added mode modeGating. - Added mode modeReducedDim.

                    Changes in version 0.1.0                        
  

• iSEEu is officially born!

IsoCorrectoR

                    Changes in version 1.4.1                        

• Modified molecule regex such that now more than 99 atoms per element can be used in the molecular formulas. Thanks to user “Farheen” by bringing up this issue on the Bioconductor support site (https://support.bioconductor.org/p/127001)

IsoformSwitchAnalyzeR

             Changes in version 1.9.5 (2020-04-22)                  

• Update type: Minor.

• Update of createSwitchAnalyzeRlist() documentation.

• Clean up of code for removal of fusion transcripts in importRdata()

             Changes in version 1.9.4 (2020-04-21)                  
  

• Update type: Minor.

• importRdata() was also updated to handle edge-case fusion transcripts.

             Changes in version 1.9.3 (2020-04-20)                  
  

• Update type: Minor.

• The creation of the switchAnalyzeRlist was updated to better handle cases where multiple isoforms have the same isoform_id (which could potentially be fusion transcripts). This was done by introducing the “removeFusionTranscripts” argument in both importGTF() and createSwitchAnalyzeRlist().

• Update date for version 1.9.3 was updated.

             Changes in version 1.9.2 (2020-04-20)                  
  

• Update type: Minor

• analyzeSignalP and its documentation was further updated to handle edge case senarios from SignalP-5 predictions.

• In extractSequence() the ‘filterAALength’ argument which removed to short and long sequences were split into to arguments: ‘removeShortAAseq’ (default is TRUE) and ‘removeLongAAseq’ (default is FALSE) to allow more nuanced control.

• Fixed a problem in extractSequence() where the onlySwitchingGenes did not work if the nuclotide/amino acid sequences was already stored in the switchAnalyzeRlist.

• extractConsequenceSummary() was modified to now also plot consequences analyzed but where no differences was found. This behaviour can be controled with the ‘removeEmptyConsequences’ argument.

• Small documentation improvements.

             Changes in version 1.9.1 (2019-10-18)                  
  

• (Version bump due to Bioconductor release)

• Update type: Minor.

• importCufflinksFiles() was updated to have the isoformNtFasta option making it easier to work with non-model organisms.

• importGTF() was updated to allow the fasta file pointed to by the isoformNtFasta argument to contain extra sequences (which are then just ignored). This is what importRdata() already did.

• Corrected a copy/paste mistake where analyzeCPC2 was suggested to be run with a codingCutoff of 0.725. This have now been corrected to 0.5
  • which was the default value all the time.

• A bug in isoformToGeneExp() which could cause problems when using Gencode data was fixed. It was also updated to give better warning message in case of different ids in the quantification and annotation.

• Due to the repport of pfam results whith missing data (which should not affect its usage within IsoformSwitchAnalyzeR) analyzePFAM() now uses readr::read_fwf() in combination with readr::fwf_empty() instead of read.table() to import the fixed width file (fwf) with the pfam results into R. analyzePFAM() will give warnings if it finds missing data.

• analyzeSignalP() was updated to better handle stand-alone versions of SignalP-5 as well as edge case senarios from SignalP-5 predictions.

• Various documentation updates.

• switchPlotTopSwitches() was updated to give better warnings for edge case senarios.

• the createSwitchAnalyzeRlist() was updated add the version number of IsoformSwitchAnalyzeR when the switchAnalyzeRlist was created.

isomiRs

                   Changes in version 1.15.2                        

FIX

• Fix error for class type when using counts method.

                   Changes in version 1.15.1                        
  

FIX

• Fix bug when dataframe is empty at isoSelect: Thanks to @DrHogart. https://github.com/miRTop/mirtop/issues/65#issuecomment-593845084

• Fix class error: using is now.

KnowSeq

             Changes in version 1.1.15 (2019-11-11)                 

• Novel Biological Based Feature Selection method named as Disease Association Feature Selection (DA-FS) added Further versions

• MAC_OS alignment tools support

• Incorporation of RUV to batch effect methods

limma

                   Changes in version 3.44.0                        

New functionality

• Add new argument package to changeLog(). changeLog() now works for any package rather than only for limma.

Code improvements

• Improved treatment of NA coefficients by contrasts.fit(). contrasts.fit() has always removed coefficients that were NA because of singularities in the design matrix, but any extra NA coefficients caused by NA expression values would cause all the stdev.unscaled values returned by contrasts.fit() to be NA for those genes. contrasts.fit() now returns non-NA coefficients and non-NA stdev.unscaled values if all the NA coefficients are multiplied by zero contrast multipliers.

• Speed improvement for contrasts.fit() if some input coefficients are not involved (have zero multipliers) in any of the contrasts.

• contrasts.fit() now preserves the pivot component of the fit object instead of removing it.

• voom now checks explicitly for NA or negative counts and gives an informative error message.

• fitFDist() now allows a covariate trend even with fewer than 4 useable observations. (Useable means positive residual df and finite variance and covariate values.)

• Internal code cleaned up to avoid partial matching of function arguments, attributes or list component names. The automatic package tests are now run with the warnPartialMatchArgs, warnPartialMatchAttr and warnPartialMatchDollar options all set to TRUE.

Documentation

• More explanation of covariates argument to removeBatchEffects().

Bug fixes

• Fix bug in contrasts.fit() when some coefficients are NA due to NA expression values and the corresponding contrast multipliers are zero. The new code fixes the improvement originally introduced in limma 3.35.9. The new code will return non-NA contrasts if the NA coefficients all get 0 weight in the contrast. Previous code was correct if all genes had the same NA coefficients but could give an avoidable NA result if some genes had NA coefficients but the first gene did not.

• Improvements to subsetting MArrayLM objects by column. Previously the presence of non-estimable coefficients sometimes caused the cov.coefficient matrix to be subsetted incorrectly; that is now fixed. Subsetting zero columns is now allowed even when F-statistics are present.

• Fix to classifyTestsF() when one or more of the coefficients have zero variance. Previously the zero variance will introduce NAs into the correlation matrix and hence cause an error. This is now avoided. This also fixes eBayes() when one or more of the coefficients are identically zero (usually caused by an all-zero contrast).

lionessR

             Changes in version 1.1.1 (2020-04-06)                  

• Fixed bug: custom function in aggregate network

Maaslin2

                    Changes in version 1.1.2                        

• Small changes to pass build tests for latest bioconductor release.

                    Changes in version 1.1.1                        
  

• Updated reference to sync up with manuscript.

maftools

                   Changes in version 2.4.00                        

BUG FIXES

• lollipopPlot2 error with zero mutation Issue: #480 - inferHeterogeneity PR #473 - oncoplot cnv crosses border #472 - Avoid wrongly naming columns in annovarToMaf Issue: #457 - Duplicated color code Issue: #452 - oncoplot with exprsTbl leads to wrong alignment Issue: #451 - plotMafSummary with single sample Issue: #449 - Avoid empty spaces and quoates while reading funcotator MAF Issue: #403 #397

ENHANCEMENTS

• OncogenicPathways improvements Issue: #505 - Added showSum, colNC, nShiftSymbols, sigSymbolsSize, sigSymbolsFontSize, pvSymbols arguments to somaticInteractions PR: #505 Thanks zmiimz - Added anno_height, drawBox, drawExtraBar arguments to oncoplot PR: #501 Thanks Kai Gu - Added decreasing argument to tcgaComapre Issue: #497
• Added startgain and startlost to annovarToMaf Issue: #487 - y_lims argument in gisticChromPlot Issue: #485 - Added support for highlighting multiple additionalFeatures Issue: #476 - Pairwise t-test and mutational load in tcgaCompare Issue: #453 - Added titleText argument to oncoplot Issue: #448 - Highlight mutated genes on gisticChromplot Issue: #443 - Added legend_height argument to oncoplot Issue: #346 - Added bgBorderCol domainBorderCol showLegend argument to lollipopPlot

NEW FUNCTIONS AND FEATURES

• tmb Simple tumor mutation burden estimation function. - setdiffMAF and intersectMAF. Set operations for MAF files. PR: #508 Thanks Shixiang Wang - tcgaDriverBP Compare genes to known TCGA drivers and their biological pathways - vafCompare plots vaf distribution of target genes from two cohorts Issue: #495 - coBarplot side-by-side barplot for maf comparison Issue: #486 - Group genes in oncoplot by specific pathways. This can be done by setting pathways = ‘auto’ or by providing a two column data.frame/tsv-file with Gene names and their corresponding pathway belongings. - Oncoplot gains rightBarData and leftBarData arguments for user specific side bar plots. - Default flatUI colors for lollipop plots

Deprecated

• geneCloud and pancanComparison

MAGeCKFlute

                    Changes in version 1.7.2                        

• Allow user customized data input.

• Prioritize the documentation.

                    Changes in version 1.6.4                        
  

• Config Travis CI test.

• Download Depmap data automatically and save as rdata.

                    Changes in version 1.6.3                        
  

• Download GO terms from source database.

• Use human genes to do enrichment analaysis in pipelines.

• Revise BatchRemove to have the same parameters as paper mentioned.

• Revise FluteRRA to surport only gene summary as input.

                    Changes in version 1.6.2                        
  

• Debug Depmap data loading process

                    Changes in version 1.6.1                        
  

• Incorporate gene id conversion between organisms into TransGeneID.

• Incorporate visualization functions from enrichplot.

• Add new functions for visualization, such as ScatterView and BarView.

• Debug the read file commands.

• Add additional document for enrichment analysis.

• Integrate Depmap data into the pipeline.

MatrixGenerics

                   Changes in version 0.0.99                        

• Added a NEWS.md file to track changes to the package.

matter

                   Changes in version 1.13.10                       

NEW FEATURES

• Added ‘s_nnzero()’ stream-stat for non-zero entries

• Added ‘push()’ and ‘pull()’ generics for future use

                   Changes in version 1.13.9                        
  

BUG FIXES

• Minor updates to ‘chunk_apply()’ internals

                   Changes in version 1.13.8                        
  

BUG FIXES

• Fixed bugs due to logical condition length > 1

                   Changes in version 1.13.7                        
  

BUG FIXES

• Fixed to internal function ‘linearInd()’

                   Changes in version 1.13.6                        
  

BUG FIXES

• Fixed bug caused by change in R 4.0 so that class of matrix is now c(“matrix”, “array”)

                   Changes in version 1.13.5                        
  

NEW FEATURES

• Support for ‘view=”chunk”’ when specifying ‘pattern’

                   Changes in version 1.13.4                        
  

NEW FEATURES

• Added ‘pattern’ argument to ‘chunk_mapply()’

                   Changes in version 1.13.3                        
  

NEW FEATURES

• Implemented ‘outfile’ argument for writing results to a file for ‘chunk_apply()’ and ‘chunk_mapply()’

                   Changes in version 1.13.2                        
  

NEW FEATURES

• Added ‘pattern’ argument to ‘chunk_apply()’

             Changes in version 1.13.1 (2019-10-30)                 
  

NEW FEATURES

• Added ‘chunk_mapply()’

mbkmeans

             Changes in version 1.3.4 (2020-03-25)                  

• Change default batch size to 500 in mbkmeans.

• Change default init_fraction to be the same as the batch size in mbkmeans.

             Changes in version 1.3.3 (2020-03-12)                  
  

• Change to blockApply to compute labels.

             Changes in version 1.3.2 (2020-02-04)                  
  

• Added option compute_labels=TRUE to optionally avoid computing labels and return only the centroids.

mCSEA

                    Changes in version 1.7.0                        

• GSEA algorithm updated to fGSEAMultiLevel method.

MEAT

             Changes in version 0.99.0 (2020-01-09)                 

• Submitted to Bioconductor

MEB

                    Changes in version 1.2.0                        

• The latest one.

                    Changes in version 1.1.0                        
  

• failed update.

metagene2

             Changes in version 1.3.3 (2019-11-13)                  

• Fixed a bug which caused overlapping contiguous regions to be assigned the wrong coverage values.

             Changes in version 1.3.1 (2019-11-05)                  
  

• Added the metagene2_heatmap function, which generates heatmap representation of the binned coverages underlying the metagene2 object.

metaseqR2

             Changes in version 0.99.2 (2020-04-22)                 

NEW FEATURES

• First submission of metaseqR2

methylGSA

                    Changes in version 1.5.9                        

• Bug fixes on Shiny app - Updated the definition of “promoter” on Shiny app

                    Changes in version 1.5.5                        
  

• In methylRRA(ORA), the overlapping between significant genes and genes in the gene set can be printed out

                    Changes in version 1.5.2                        
  

• Updated the definition of “promoter”

                    Changes in version 1.5.1                        
  

• Minor updates on package vignette

methylKit

                   Changes in version 1.13.4                        

IMPROVEMENTS AND BUG FIXES

• set stringAsFactors to FALSE - changed when reading data and tabix files - this solves class missmatches downstream - update methylKit data with stringsAsFactors off

• methRead: - filter for given context when pipeline is cytosinereport
  • order data when processing with methread, this ensures that methylRaw and methylRawDB contain exact same data - add additional test for methread, check whether methread with or without tabix produces same data when processing bismark coverage and cytosine report

• unite: - make sure .CpG.dinuc.unifyOld equals .CpG.dinuc.unify - add test to check that destranding result is same for methylBase and methylBaseDB

                   Changes in version 1.13.3                        
  

IMPROVEMENTS AND BUG FIXES

• getMethylDiff: - fixes bugs in method for methylDiffDB - suffix will be actual type now, was “type” before - removed whitespaces in filename, fixes https://github.com/al2na/methylKit/issues/171 - add extensive test for getmethylDiff function

• applyTbxByChunk: - Allow optional writing of colnames and rownames if returntype is text. Find details in https://github.com/al2na/methylKit/issues/169

• percMethylation: - return rownames for methylDB when rowids is TRUE, fixes https://github.com/al2na/methylKit/issues/170 - add extensive tests for percMethylation

• reorganize: - fix bug in method for methylBaseDB introduced with new tabix header - add extensive testing for reorganize

• assocComp: - add further checks for proper annotation

• removeComp: - set default comp to NULL, to trigger earlier fail - fix bug method for methylBaseDB introduced with new tabix header

• reconstruct: - update checks for percent methylation matrix - fix bug with fread

• add extensive tests for batch control functions

• diffMethPerChr: - prevent from plotting when no chrom left - add extensive tests for diffMethPerChr

                   Changes in version 1.13.2                        
  

IMPROVEMENTS AND BUG FIXES

• fread.gzipped: - add pre-checks wheter file exists and is not empty - switch to R.utils::gunzip instead of building shell command manually

• tileMethylCounts: remove orphan warning triggered by incomplete temporary methylRaw object, fixes https://github.com/al2na/methylKit/issues/175

• update vignette: - add mincov argument to methread - add paragraph to tiling section about reducing coverage threshold + update example code

• update docs: - rebuild docs with more recent version of roxygen - exclude examples from internal function

• increase version requirement for tabix files with header

                   Changes in version 1.13.1                        
  

IMPROVEMENTS AND BUG FIXES

• fix issues related to build checking: - logical vectors of size longer than one - docs for methseg contain line longer than 100 chars

• fix methSeg2bed error when seg.mean=0 and scores=NA by replacing score with zero if average seg.mean is zero https://github.com/al2na/methylKit/issues/123

• update vignette: - explain how to get wig/bigwig file from methylKit https://github.com/al2na/methylKit/issues/157 - explain how to deal with soft clipping in processBismarkAln https://github.com/al2na/methylKit/issues/159 - add section about exporting and loading tabix objects starting from version 1.13.1

methylSig

             Changes in version 0.99.0 (2020-03-23)                 

• Refactor functions and workflow from pre-0.99.0 releases o methylSigReadData() replaced with the functions: o bsseq::read.bismark() o filter_loci_by_coverage() o filter_loci_by_location() o methylSigTile() replaced with the functions: o tile_by_regions() o tile_by_windows() o Differential testing should be preceded with: o filter_loci_by_group_coverage() o binomialDiffCalc() is replaced by diff_binomial() o methylSigCalc() is replaced by diff_methylSig() o methylSigDSS() is replaced by diff_dss_fit() and diff_dss_test()

• See “Using methylSig” vignette for full example.

• See “Updating methylSig Code” vignette for how to retrofit pre-0.99.0 code.

MetNet

             Changes in version 1.5.3 (2020-03-09)                  

• change tests for rtCorrection, do not use function levels to test for if +, . or ? is present in the transformation list

• update vignette that formulas are displayed properly

             Changes in version 1.5.2 (2020-01-12)                  
  

• change unit tests for clr and aracne that it doesn’t fail in Windows

• change ppm calculation in structural, use m/z of precursors instead of m/z differences

• change unit tests for clr and aracne that it doesn’t fail in Windows

             Changes in version 1.5.1 (2019-12-05)                  
  

• rename combineStructuralStatistical to combine

• combine accepts directly the output of createStructuralAdjacency, before the function combineStructuralStatistical accepted a numeric matrix (first entry of the output of createStatisticalAdjacency)

• remove the functions consensusAdjacency, createStatisticalAdjacency, createStatisticalAdjacencyList

• add functions statistical, getLinks, topKnet, threshold with improved functionality for thresholding the statistical adjacency matrices (based on hard thresholds, or top1, top2 or mean consensus matrix calculation according to Hase et al.) to replace removed functions

• rename createStructuralAdjacency to structural

• change vignette to markdown

• add parameter directed in structural to allow for directed networks

• add parameter values to specify if respectively min, max or all values from the corresponding feature pairs (in the upper and lower triangle) should be taken in statistical

microbiome

             Changes in version 1.9.9 (2019-12-25)                  

• noncore_members removed

• Added aggregate_rare function

• Bioc polishing

             Changes in version 1.9.2 (2019-12-25)                  
  

• Divergence function rewritten for clarity * Switched from sapply to vapply

• Removed noncore_abundance

• Fixing plot_core axis labeling

• is.compositional function added

• spreadplot function added

• removed ready made themes from functions

• Renamed is.compositional to is_compositional

• Fixed a bug in core_members (also non-compositional detection now allowed)

• removed rm.na option from aggregate_taxa

• Deprecating noncore_* functions (replacing with rare_* functions everywhere)

• Removed variable_members function

• Support removed from R-3.3.3 and lower

microbiomeDASim

             Changes in version 1.1.6 (2020-03-10)                  

• F1000 manuscript with package details accepted and available at https://doi.org/10.12688/f1000research.20660.2

• Citation updated within package

• Require study duration be specified when simulating observations

• Implemented functionality to allow random asynchronous timepoints samples along the study duration

• Additional functions to approximate observed longitudinal microbiome data

• Convert simulated data into common data objects in either the metagenomeSeq or phyloseq packages

• Existing function changes:

• gen_norm_microbiome (must specify t_interval for study duration and additional option to specify asynchronous time points using asynch_time=TRUE)

• mvrnorm_sim (must specify t_interval for study duration and additional option to specify asynchronous time points using asynch_time=TRUE)

• New functions:

• conversion_functions (convert simulated data to metagenomeSeq or phyloseq object)

• sim_obs_functions (host of functions that allow users to specify discrete sampling timepoints and approximate observed longitudinal patterns)

miRSM

                    Changes in version 1.5.1                        

• Update miRSM function <2020-02-01, Sat>

miRspongeR

                Changes in version 1.13.1-1.13.2                    

• Update vignettes <2020-03-25, Wed>.

missMethyl

                   Changes in version 1.21.4                        

• Bug fix: Fixed bug that resulted in negative value for odds. Bug only occurred in rare cases when CpG universe was smaller than all CpGs on array AND if some large collections had more genes than the universe.

                   Changes in version 1.20.3                        
  

• Added fract.counts logical parameter to enable fractional counting of CpGs to be turned off in gometh, gsameth, goregion and gsaregion. This switches off the adjustment for CpGs that map to multiple genes. This is primarily intended for comparison with earlier versions and we strongly encourage it to be set to TRUE.

mitch

                   Changes in version 0.99.15                       

• Making changes in response to bioconductor review

                    Changes in version 0.2.2                        
  

• Test

mixOmics

                   Changes in version 6.12.0                        

new features / enhancements

• circosPlot and plotLoadings bug caused by features with NAs fixed - circosPlot’s inconsistentcy of blocks with identical X names fixed - consensus and weighted consensus plots now supported for plotIndiv with relevant block analyses - plotLoadings’s feature name trimming can be customised - block.splsda bug which could drop some Y factors with near.zero.variance=TRUE fixed - perf.block.splsda now supports calculation of combined and per-block AUC - model improvement significance can be custmoised in all perf and tune functions - perf.block.splsda is now much faster and supports FORK clusters - tune.(s)pls(da), perf.(s)plsda now support FORK clusters

bug fixes

• plotIndiv(…, ind.names = FALSE) warning/bug fixed - tune.block.splsda bug on Windows parallelisation fixed - perf and tune functions’ issue when choosing the optimum component resolved - added option to suppress auroc from printing all the AUCs

MLInterfaces

                   Changes in version 1.67.10                       

• Fix es2df (for R 4.0.0) setting stringsAsFactors = TRUE

• Add unit test

                   Changes in version 1.67.1                        
  

• rda has been moved to ‘Enhances’ and its use is conditional its presence <2019-01-05>

Modstrings

             Changes in version 1.3.9 (2019-03-02)                  

• added incompatibleModifications(), which returns a logical for manual subsetting

• added combineModifications() to allow modifications to be combined manually

• added separate() for GRanges to allow modification to be separated, if possible

             Changes in version 1.3.4 (2019-02-05)                  
  

• added removeIncompatibleModifications()

             Changes in version 1.3.3 (2019-02-05)                  
  

• combineIntoModstrings() is now ‘vectorized’ for multiple sequences. Sequences with the same name are treated independently and are modified equally

• add stop.on.error option for combineIntoModstrings()

             Changes in version 1.3.2 (2019-12-01)                  
  

• Display ModDNA and ModRNA sequences in color

MOMA

             Changes in version 1.0.0 (2020-04-22)                  

• Bioconductor Initial Release

MotifDb

                    Changes in version 1.30                         

NEW FEATURES

• now has HOCOMOCO version 11, with all motifs classified, and queryable, by category (“core”, “secondary”) and reliability (A, B, C, D).

motifStack

                   Changes in version 1.31.2                        

• reduce the compiling time for vignettes.

                   Changes in version 1.31.1                        
  

• fix the issue invloved by replace class(x)==”something” to is(x, “something”).

MsCoreUtils

                    Changes in version 0.99                         

MsCoreUtils 0.99.3

• Trigger build.

MsCoreUtils 0.99.2

• Provide more comprehensive description. - Add vignette.

MsCoreUtils 0.99.1

• Additional functions, and using Author@R to specify (unique) RforMassSpectrometry Package Maintainer.

MsCoreUtils 0.99.0

• First release of MsCoreUtils with core function to get extreme values, grouping/matching, noise/smoothing, similarity measurements, various helper function, and function to process (impute and normalise) quantitative features.

MSnbase

                    Changes in version 2.13                         

Changes in 2.13.9

• Typo in OnDiskMSnExp man page <2020-04-26 Sun> - Fix plot,[On]MSnExp for centroided data <2020-04-26 Sun> - Use free x scaling in plot,MSnExp’s facet <2020-04-26 Sun>

Changes in 2.13.8

• Remove duplicated COM= when writing mgf <2020-04-24 Fri>

Changes in 2.13.7

• Make writeMgfData example runnable <2020-04-20 Mon> - Fix issue when writing mgf with a connection (PR #505, by Rico Derks) <2020-04-20 Mon> - Add writeMgfData file/connection unit test <2020-04-20 Mon>

Changes in 2.13.6

• When reading MzTab files, the column names aren’t converted to legal colnames (my make.names) - check.names in read.delim is now (internally) set to FALSE. This will make it easier to write MzTab objects back to files. See issue #501 for a discussion. - Re-introduce MzTab write support (contributed by Steffen Neumann). See #502.

Changes in 2.13.5

• Support reading of MzTab-M 2.0 format (contributed by Steffen Neumann). - Use UTF-8 encoding.

Changes in 2.13.4

• Fix failing unit test: in R 4.0, data.frames not don’t cast strings to factors anymore <2020-03-24 Tue>

Changes in 2.13.3

• exprsToRatios is now defunct.

Changes in 2.13.2

• Need ProtGenerics 1.19.3 for impute generic

Changes in 2.13.1

• Need ProtGenerics 1.19.2 - Deprecate filterZero and exprsToRatios

Changes in 2.13.0

• Bioconductor 3.11 (devel)

msPurity

                   Changes in version 1.13.2                        

• Update dev to match bug fixes in master

                   Changes in version 1.13.1                        
  

• Update dev to match bug fixes in master

                   Changes in version 1.13.0                        
  

• Bioconductor dev (automatic version bump)

                   Changes in version 1.12.2                        
  

• Fix to allow large files to be processed with combineAnnotation (in some cases the summary report should be excluded)

                   Changes in version 1.12.1                        
  

• Bug fix for combineAnnotations - MS1 lookup not handling CAMERA adducts correctly

• Fillpeaks bug fix see github #68

• Documentation fixes

MSstatsTMT

             Changes in version 1.4.7 (2020-04-24)                  

• Update the NEWS file

             Changes in version 1.4.6 (2020-04-14)                  
  

• Fix bug in groupComparison() for unbalanced design

• Use df approximation from lmerTest to perform group comparison

             Changes in version 1.4.5 (2020-03-01)                  
  

• Add new function OpenMStoMSstatsTMTFormat()

             Changes in version 1.4.4 (2020-02-01)                  
  

• Fix bug in PDtoMSstatsTMTFormat(): remove redundant rows when combining multiple fractions

             Changes in version 1.4.3 (2019-12-28)                  
  

• Fix bug in groupComparisonTMT(): very few measurements case previously doesn’t work

             Changes in version 1.4.2 (2019-12-20)                  
  

• Add the column ‘issue’ to the output of groupComparisonTMT()

             Changes in version 1.4.1 (2019-10-31)                  
  

• Fix the bug in the PDtoMSstatsTMTFormat() due to different PD version

MultiAssayExperiment

                   Changes in version 1.14.0                        

New features

• exportClass creates a number of .csv data files for exporting data
• Allow vector input i for selecting assays in longFormat (@lgatto, #266) - Updates to ‘Using MultiAssayExperiment with DelayedMatrix’ vignette

Bug fixes and minor improvements

• Warn when colData rownames and ExperimentList colnames are empty (@LTLA #262)
• Add informative error message for ExperimentList (@lgatto, #265)
• Informative warning when dropping ExperimentList element columns (@lwaldron)
• Fixes to constructor functions, MultiAssayExperiment and MatchedAssayExperiment (@lgatto, #267 #268, @lwaldron)
• Add warning when j in mae[i, j, k] is longer than colData rows
• Strict argument matching between generic and methods
• Updates due to class(matrix())
• UpsetSamples more robust to differences in names between split sampleMap and names(ExperimentList) (@jonocarroll, #269)
• Refactored and improved UpsetSamples
• ExperimentList propagation of mcols and metadata (@vobencha, #270)
• Enforcement of validObject with replacement methods colData and sampleMap (@vobencha, #271)

mzR

                   Changes in version 2.21.1                        

• inject a new PSI-MS.obo controlled vocabulary data-version: 4.1.30 date: 30:08:2019 16:10 saved-by: Gerhard Mayer

NADfinder

                   Changes in version 1.11.1                        

• replace all class by is.

NBAMSeq

             Changes in version 1.3.1 (2020-02-18)                  

• The default gamma parameter in NBAMSeq changed from 2 to 2.5.

• The NBAMSeq function now supports fitting linear model after fitting GAM model.

netDx

             Changes in version 0.99.0 (2019-11-11)                 

• Submitted to Bioconductor

ngsReports

                    Changes in version 1.3.3                        

• Added line plot to plotDupLevels()

                    Changes in version 1.3.2                        
  

• Changed default template to use DT instead of kable for tables and removed kableExtra dependency

• Added outputDir as an argument to writeHtmlReport()

normr

                   Changes in version 1.13.1                        

• Changed deprecated ‘GenomeInfoDb::fetchExtendedChromInfoFromUCSC’ to ‘GenomeInfoDb::getChromInfoFromUCSC’

NPARC

             Changes in version 0.99.0 (2019-10-29)                 

• Submitted to Bioconductor

omicplotR

                    Changes in version 1.7.1                        

• bug fix to cause by Shiny 1.4.0 (renderDataTable causes error in jquery). solution is to import DT package and specify DT::renderDataTable and DT::dataTableOutput.

• ensured that ALDEx2 dependency for aldex.plot feature is correctly implemented

• added Brandon Lieng as author

                    Changes in version 1.7.0                        
  

• bioconductor dev version 3.11, no changes since 1.5.4

OncoSimulR

            Changes in version 2.17.92 (2020-04-27)                 

• Fixed test.Z-magellan failure in Mac.

            Changes in version 2.17.91 (2020-04-24)                 
  

• Fixed Wrestrict warnings in Windows from MAGELLAN’s sources.

             Changes in version 2.17.9 (2020-03-16)                 
  

• With R-devel, stringsAsFactors = FALSE by default. Fix tests

• POM documentation.

             Changes in version 2.17.8 (2020-02-02)                 
  

• With newest R-devel (01-28) getting “the condition has length > 1”: fixed.

             Changes in version 2.17.7 (2020-01-30)                 
  

• Removed dependency on nem, to be deprecated. Adding nem’s code (file nem_transitive_reduction.R).

             Changes in version 2.17.6 (2020-01-22)                 
  

• Further additions of MAGELLAN’s functionality and Additive model to rfitness

             Changes in version 2.17.5 (2019-12-19)                 
  

• Oooops: forgot Makevars.win

             Changes in version 2.17.4 (2019-12-19)                 
  

• fno-common: better way of dealing with verbose in magellan.

             Changes in version 2.17.3 (2019-12-17)                 
  

• Compiles with fno-common (for gcc 10).

             Changes in version 2.17.2 (2019-12-17)                 
  

• Fixed error “length(x) = 5 > 1’ in coercion to ‘logical(1)’”

             Changes in version 2.17.1 (2019-11-24)                 
  

• rfitness: clarified log=TRUE and truncate_at_0 after log.

• Magellan_stats: really return a vector.

             Changes in version 2.17.0 (2019-10-25)                 
  

• Bumped version for BioC-3.11

openCyto

                    Changes in version 3.11                         

Enhancements

• Allow control of mininum number of events for each step of GatingTemplate #298

Bug Fixes

• Handle a few more edge cases in .improvedMinDensity - Added a fix to the density estimate used by gate_tautstring

                    Changes in version 3.10                         
  

API Changes

Simple renaming

• gate_flowClust_1d -> gate_flowclust_1d - gate_flowClust_2d -> gate_flowclust_2d - tautStringGate -> gate_tautstring - templateGen -> gh_generate_template - add_pop_init -> gs_add_gating_method_init - add_pop -> gs_add_gating_method - remove_pop -> gs_remove_gating_method - get.helperGates -> gs_get_helpergates - toggle.helperGates -> gt_toggle_helpergates - delete.helperGates -> gs_delete_helpergates - getNodes -> gt_get_nodes - getParent -> gt_get_parent - getChildren -> gt_get_children - getGate -> gt_get_gate - gating -> gt_gating - registerPlugins -> register_plugins - Classes and methods no longer exported

• registerGatingFunction - gtMethod - gtPopulation - polyFunctions - ppMethod

Bug Fixes

• Some minor fixes to gt_toggle_helpergates - Fix “positive” argument to gate_mindensity to match doc

oposSOM

                    Changes in version 2.5.2                        

• Bugfix for class(…) error occuring in R > 4.0.0

                    Changes in version 2.5.1                        
  

• Minor bugfixes

                    Changes in version 2.5.0                        
  

• Version bump of Bioconductor

ORFik

                   Changes in version 1.7.17                        

SIGNIFICANT USER-VISIBLE CHANGES

• Added pmapToTranscriptsF, a much faster pmapToTranscripts.

• All of ORFik now supports weights for representing duplicated reads. This will speed up all function related to NGS data a lot.

                    Changes in version 1.7.0                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• The ORFik experiment syntax is ready, to simplifiy ORFik usage with big data.

packFinder

             Changes in version 1.0.0 (2020-04-25)                  

• Minor bugfixes

• Generate package graphics

• Allow for partial TSD matching

• Add methods for BLAST classification

• Add method to collapse overlapping sequences

             Changes in version 0.99.0 (2019-10-28)                 
  

• Package Submitted to Bioconductor

• Core package functionality implemented

PAST

             Changes in version 1.2.8 (2020-03-16)                  

• fixed warnings from missing documentation

             Changes in version 1.2.7 (2020-03-11)                  
  

• brought documentation in line with code

             Changes in version 1.2.6 (2020-03-11)                  
  

• fixed a warning in plot_pathways

             Changes in version 1.2.5 (2020-03-10)                  
  

• fixed an error in loading large annotations

             Changes in version 1.2.4 (2020-03-04)                  
  

• brought code in line with documentation

             Changes in version 1.2.3 (2020-02-27)                  
  

• added correct citation after paper publication

             Changes in version 1.2.1 (2019-12-17)                  
  

• minor corrections to package based on original method

PCAtools

                    Changes in version 2.0.0                        

• added parallelPCA function to perform Horn’s parallel analysis, which chooses an ideal number of principal components to retain (courtesy Aaron Lun)

• added findElbowPoint function, which finds the elbow point in the curve of variance explained and which can also be used to determine the number of principal components to retain (courtesy Aaron Lun)

• user can now specify custom labels for points

• fixed bug with singlecol parameter for biplot colouring everything black

• added p-value adjustment for eigencorplot (aleighbrown)

• eigencorplot now automatically converts non-numeric columns to numeric (aleighbrown)

peakPantheR

             Changes in version 1.1.2 (2020-04-05)                  

• Correct test tolerance for Win on R 4.0.0

             Changes in version 1.1.1 (2020-03-04)                  
  

• Compatibility with R 4.0.0

peco

            Changes in version 0.99.16 (2020-04-10)                 

Bug fixes

• Fix AppVeyor build (use R release) - Fix Travis build (use R release) - Require R >= 2.10 - Ignore Rmd-related files when building package

            Changes in version 0.99.15 (2020-04-08)                 
  

Minor changes

• Relaxed minimum versions for dependencies

            Changes in version 0.99.14 (2020-03-23)                 
  

Bug fixes

• Tavis-CI and AppVeyor

            Changes in version 0.99.13 (2020-03-23)                 
  

Bug fixes

• Debug cycle_npreg_outsample example

Bug fixes

• Debug vignettes.Rmd

            Changes in version 0.99.11 (2020-03-23)                 
  

Major changes

• Rename fit_trendfilter_generic to fit_trendfilter

             Changes in version 0.99.7 (2020-01-01)                 
  

Major changes

• Backward compatibiltiy with R3.5.0

             Changes in version 0.99.6 (2020-01-01)                 
  

Major changes

• Inclue new vignette example

Bug fixes

• Debug cycle_npreg_outsample and data_transform_quantile

             Changes in version 0.99.3 (2019-09-19)                 
  

Major changes

• cycle_npreg_outsample outputs SingleCellExperiment object - data_transform_quantile inputs and outputs SingleCellExperiment object

Bug fixes

• @import and @importFrom fields - BiocCheck notes

Major changes

• Store data in SingleCellExperiment objects

             Changes in version 0.99.1 (2019-09-16)                 
  

Bug fixes

• R CMD Check warnings and errors - R CMD BiocCheck warnings and errors

             Changes in version 0.99.0 (2019-09-11)                 
  

Submitted to Bioconductor

phantasus

                    Changes in version 1.7.6                        

• Fix bug after change to stringAsFactors=FALSE

                    Changes in version 1.7.4                        
  

• Removed Matrix.utils dependency

                    Changes in version 1.7.3                        
  

• Volcano plot tool

                    Changes in version 1.7.2                        
  

• Better GEO loader

• DESeq2 experimental support

• Initial support for hierarchical preloaded folder

PhyloProfile

                   Changes in version 1.1.12                        

• Added pseudo IDs for Holozoa and Holomycota clades and their non-NCBI sub-clades

                   Changes in version 1.1.11                        
  

• Increased the resolution of the phylostratigraphy function

                   Changes in version 1.1.10                        
  

• Improved the rank indexing function

                    Changes in version 1.1.6                        
  

• Removed grDevices, grid, stats, utils from Imports list in DESCRIPTION

                    Changes in version 1.1.5                        
  

• Added progress indicators for data loading and processing steps

• Removed shinycssloaders

                    Changes in version 1.1.3                        
  

• Fixed bug listing taxa by selecting a supertaxon from a higher level

• Added message for downloading preprocessed data

                    Changes in version 1.1.2                        
  

• Fixed bug sorting taxa when taxonomy rank is set as strain

                    Changes in version 1.1.1                        
  

• Commented examples of OMA parser functions

• Turned off tests for OMA parser functions

Pigengene

            Changes in version 1.13.14 (2020-03-03)                 

Changes in existing functions

• inherits(a, b) is now used instead of class(a)==b.

             Changes in version 1.13.6 (2020-01-03)                 
  

Changes in existing functions

• doSave was added to the combine.networks() function.

             Changes in version 1.13.4 (2019-11-19)                 
  

Bug Fixes

• In the combine.networks() function, the netwok typo was fixed.

plgem

                   Changes in version 1.59.2                        

• bug fixes: –fixed syntax error in plgem.obsStn' --imported function is’ into NAMESPACE

                   Changes in version 1.59.1                        
  

• bug fixes: –updated class-checks to avoid package failures in R 4.0, as reported in https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html and http://bioconductor.org/developers/how-to/troubleshoot-build-report/#classEq –imported several functions into NAMESPACE from grDevices', graphics’ and `stats’

plyranges

                   Changes in version 1.7.16                        

• refactoring of select internals, improved speed when casting a GRanges -> DataFrame

                   Changes in version 1.7.15                        
  

• further fixes to reduce/disjoin internals

                   Changes in version 1.7.14                        
  

• fixes reduce/disjoin internals cleans up disjoin cases when an expansion occurs

                   Changes in version 1.7.13                        
  

• set tidyselect version to be v 1.0
• set coverage method for delegating ranges

• fix docs for bam reading

                   Changes in version 1.7.11                        
  

• move from tidyselect::vars_select() to tidyselect::eval_select()

                    Changes in version 1.7.7                        
  

• update handling of list columns, expand_ranges() no longer takes cartesian product if lists are parallel. summarize() properly handles list column output without blowing out number of columns.

                    Changes in version 1.7.6                        
  

• adds method for dplyr::sample_n()

                    Changes in version 1.7.5                        
  

• fixed issue #62 for Ranges construction, the as_granges() and as_iranges() functions now handle List columns correctly

• added in helper functions for dealing with names in Ranges. See ?ranges-names for details.

                    Changes in version 1.7.4                        
  

• added slice() for Ranges, and GroupedRanges
• internals of grouping have been overhauled, but there shouldn’t be any user facing changes. It is now much faster to generate groupings.
• group information can be interrogated with dplyr::group_keys()
• a GRangesList can be obtained automatically from a GroupedGenomicRanges with dplyr::group_split()

• group indices can be generated with dplyr::group_indices()

                    Changes in version 1.7.3                        
  

• shift_downstream() and shift_upstream() now properly handle vector amounts of shift. Fixes issue #73

                    Changes in version 1.7.2                        
  

• Left outer join overlap operations now work if either x or y have no metadata columns see #70
• Left outer join overlap operations will also correctly behave in situations when there are no non-overlapping ranges.
• Left outer join overlaps no longer modify seqinfo see here

• patch left outer join when x or y are IRanges, flesh out overlaps documentation.

                    Changes in version 1.7.1                        
  

• Reformatting NEWS.md so no longer softlinks to inst/NEWS

pmp

                   Changes in version 0.99.6                        

• Updated vignettes.

                   Changes in version 0.99.2                        
  

• Support for SummarizedExperiment class.

• Updated documentation and vignette.

• Added functions for QCRSC algorithm of signal-batch correction for MS data.

                    Changes in version 0.2.6                        
  

• glog transformation can use fixed lambda value input.

• Plot to visualise output of glog lambda value optimisation.

                    Changes in version 0.2.5                        
  

• Pre-calculated mean reference values can be used with PQN normalisation function.

             Changes in version 0.2.4 (2019-08-07)                  
  

• Updated documetation and usage examples.

• Refactored glog scaling function.

• PQN normalisation supports using all samples to calculate correction factor.

podkat

                   Changes in version 1.19.1                        

• fix in nullModel() method to ensure compatibility with R 4.0

                   Changes in version 1.19.0                        
  

• new branch for Bioconductor 3.11 devel

polyester

                   Changes in version 1.99.3                        

• NB function now exported

• note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

                   Changes in version 1.99.2                        
  

• bug fix in fragment generation (last 2 bases of transcript were never sequenced)

proDA

                     Changes in version 1.1                         

• Only convert 0’s to NA’s if there are no NA’s in the dataset (commit 06df44a, fix issue #3)

pRoloc

                    Changes in version 1.27                         

Changes in version 1.27.6

• Depend on MLInterfaces 1.67.10

Changes in version 1.27.5

• import stats4::plot <2020-03-26 Thu>

Changes in version 1.27.4

• Import missing mclust::mclustBIC

Changes in version 1.27.3

• Remove exprsToRatio man page (function in MSnbase and is deprecated)

Changes in version 1.27.2

• Fix errors related to R-devel

Changes in version 1.27.1

• Merged plotting payes PR

Changes in version 1.27.0

• Version bump for Bioc 3.11 (devel)

pRolocGUI

                    Changes in version 1.21                         

CHANGES IN VERSION 1.21.3

• Depend on latest pRoloc

CHANGES IN VERSION 1.21.2

• Keep only one maintainer

CHANGES IN VERSION 1.21.1

• Update email

ProtGenerics

                   Changes in version 1.19.3                        

• new impute generic

                   Changes in version 1.19.2                        
  

• new filterNA generic

                   Changes in version 1.19.1                        
  

• new aggregateFeatures generic

psichomics

                   Changes in version 1.12.1                        

• Alternative splicing events can now be represented via diagrams: - Redesign of alternative splicing event selection (graphical interface) - plotSplicingEvent() plots diagram representation of alternative splicing events - In the visual interface, alternative splicing event diagrams were added below distribution plots (to quickly illustrate higher and lower values of alternative splicing quantification) and in annotation page - User-provided junction quantification loading: - Support junction coordinates from mitochondrial, Z and W chromosomes - Fix issues with files containing splice junctions within random, alt and unknown chromosomes by discarding those rows (a warning is raised) - Alternative splicing annotation: - listSplicingAnnotations() can now be filtered by species, assembly and data of available annotations - Improve import/export of data groups from/to a file, including colour support
• Copy-edit and improve all tutorials, welcome message and help tab - Include link to article in Methods in Molecular Biology: https://doi.org/10.1007/978-1-0716-0301-7_10

More bug fixes and minor changes

• TCGA and SRA data loading: - loadFirebrowseData() now returns expected data when asking for multiple datasets (such as in the case of performing a pan-cancer analysis) in both visual and command-line interface - SRA projects containing only one column of extra information in sample metadata are now correctly loaded instead of raising an error (loadSRAproject()) - Data loading and manipulation:
• Copy-edit information on the format of user-provided files - Warn when discarding rows with duplicated rownames after loading user-provided files - getGtexDataTypes() is now exported, as expected
• parseSplicingEvent() now returns the coordinates as numeric if coords = TRUE and char = FALSE - Improve dialog when trying to load a local folder without any supported files available - Alternative splicing annotation: - Confirmation dialog is not displayed any more when creating a folder (specially useful while running the visual interface) - Allow to select cache directory of AnnotationHub (command-line interface) - Fix prepareGeneQuant() discarding the argument strandedness if either stranded or stranded (reverse) - Data grouping: - Samples not associated with any subject are now kept when exporting groups to a file - Fix issues related with importing groups based on a file with groups of splicing events and/or genes - Inform user when groups are successfully loaded from a file and whether any group elements are discarded in the process - Show number of genes contained in pre-made gene lists - Discard unavailable genes when creating group of genes based on pre-made gene lists (unless these are automatically created at startup) - Density plot (plotDistribution()): - Fix visual bug when plotting a group with only one sample (if one data point is available for a group, only the rug plot is drawn) - After hiding all plot series, rug plots of the different groups can be distinguished based on the Y axis (different arbitrary Y values are given to each rug plot series) - Rug plot labels now show data values if sample names are not provided - Rug plot labels can now be rotated (rotation is not enabled by default given Highcharts issues that may occur at different zoom levels and depending on proximity between different sample values) - Fix misguiding example in function documentation - When hovering the values in the rug plot, the colour of the tooltip is now the same used for the rug points as expected - Survival analysis (p-value plot): - Fix alternative splicing quantification cutoff being selected based on the one whose difference has the highest (instead of the lowest) p-value - Fix plot line label presenting “p < 0.05” independently of the threshold used for significance - Gene, transcript and protein annotation: - Show available annotation information and query PubMed even if Ensembl is down - Avoid app crash when searching for PubMed articles too many times - Improve warning/error alerts: - Fix alerts crashing the visual interface - Improve message formatting regarding HTML-containing alerts - Improve unit tests and function documentation

PureCN

                   Changes in version 1.18.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• callAlterations: columns C and seg.mean now provide the values of the segment listed in seg.id. This changes the behaviour in cases where the gene contains breakpoints and thus multiple segments overlap (#112)

BUGFIXES

• Fix for bug that can result in crash when candidates were provided in runAbsoluteCN and test.purity, max.ploidy and/or min.ploidy were set to non-default values

qcmetrics

                    Changes in version 1.25                         

CHANGES IN VERSION 1.25.1

• update email

qpgraph

                    Changes in version 2.22                         

USER VISIBLE CHANGES

• Added new function filterCollinearities() to aid in identifying and discarding collinear pairs of variables/genes.

qsmooth

             Changes in version 1.3.1 (2020-03-01)                  

• Fixed bug on conditionals longer than 1

RaggedExperiment

                   Changes in version 1.12.0                        

Bug fixes and minor improvements

• Adjust to changes from SummarizedExperiment::assay (withDimnames argument) - Reference simplifyTCGA helper function from TCGAutils in examples - Restore original real-world qreduceAssay example and include alternative qreduceTCGA example

randRotation

            Changes in version 0.99.12 (2020-04-25)                 

• Submitted to Bioconductor

Rbowtie

                   Changes in version 1.27.1                        

NEW FEATURES

• updated bowtie to version 1.2.3 (now also supports bowtie2 indices and compilation on intel, gcc 8 and gcc 9)

RcisTarget

                     Changes in version 1.7                         

• New function: reRank

• ImportRankings: Added arguments “indexCol” and “warnMissingColumns”

• Class rankingRcisTarget: Added methods rownames and colnames

• Support for .parquet databases

RCy3

                    Changes in version 2.8.0                        

• New functions: - mergeNetworks - analyzeNetwork

• Better messaging for… - App-related functions, like installApp - When style changes are applied to “default” style

ReactomeGSA

             Changes in version 1.1.4 (2020-04-20)                  

• bioRxiv paper is out!

             Changes in version 1.1.3 (2020-04-11)                  
  

• Added custom function to calculate average cluster expression for Seurat objects

             Changes in version 1.1.2 (2020-03-13)                  
  

• Add support manually track the status of submitted analyses

• Added additional signature to add_dataset to support expression values as matrix

             Changes in version 1.1.1 (2020-02-19)                  
  

• Compress JSON requests using gzip to improve performance for large datasets

receptLoss

             Changes in version 0.99.8 (2020-03-01)                 

• Updated bug in ‘toMatrix’ function in scripts.R, allowing it to accept the objects with multiple classes

             Changes in version 0.99.6 (2020-03-01)                 
  

• Updated the ‘toMatrix’ function in scripts.R, allowing it to accept the RangedSummarizedExperiment class, and added option for specifying rownames

             Changes in version 0.99.5 (2020-02-14)                 
  

• update .Rbuildignore

             Changes in version 0.99.4 (2020-02-12)                 
  

• removed .Rproj files from git repo

• Updated gitignore file to include .Rproj files

             Changes in version 0.99.3 (2020-02-12)                 
  

• removed .DS_Store and .Rproj files from git repo

             Changes in version 0.99.2 (2020-02-12)                 
  

• exported ‘toMatrix’ function to fix R CMD check error.

             Changes in version 0.99.1 (2020-02-11)                 
  

• As per Martin Morgan’s feedback from BioConductor review, added a function, ‘toMatrix’, to accept SummarizedExperiment and other matrix-like objects

             Changes in version 0.99.0 (2020-02-05)                 
  

Changes:

• Passed R CMD Check and devtools::build() - Submitted to Bioconductor

reconsi

                   Changes in version 0.99.2                        

• Reducing runtimes examples

                   Changes in version 0.99.1                        
  

• Semantic changes by Joris Meys

                   Changes in version 0.99.0                        
  

• Submission to BioConductor

                    Changes in version 0.1.2                        
  

• Prior weights for bootstrap samples modified

                    Changes in version 0.1.1                        
  

• Enforce normality assumption on resample instances and collapsed null

recount

                   Changes in version 1.13.2                        

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://leekgroup.github.io/recount/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

                   Changes in version 1.13.1                        
  

• Mention in reproduce_ranges() the link to https://support.bioconductor.org/p/126148/#126173 which shows how to update the gene symbols in the RSE objects in recount.

regionReport

                   Changes in version 1.21.11                       

BUG FIXES

• Cropping images through magick::image_trim() as done by default by BiocStyle::html_document() can fail on Linux. This could be an ImageMagick issue or an issue about lack of resources. The full investigative report is at https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016650.html. This is related to: https://github.com/yihui/knitr/issues/1785#issuecomment-574723631 https://github.com/yihui/knitr/issues/1796 https://github.com/Bioconductor/BiocStyle/issues/65#issuecomment-552832630 https://github.com/ropensci/magick/issues/171 https://github.com/ropensci/magick/issues/194 In regionReport version 1.21.10 I have opted by using crop = NULL to disable cropping of images by BiocStyle::html_document() and thus avoid the issues with ImageMagick either coming from magick, from the version of ImageMagick installed on the Linux Bioconductor build machine and devel docker, or from resources in these two Linux environments as described in the investigative report. About a month ago I also saw failures on Windows on Bioc 3.10. Whether they were caused by ggbio 1.35.1 or this issue will remain a mystery. But it’s likely that this magick::image_trim() issue also affected the Bioconductor windows builder. The related bioc-devel threads are: https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html https://stat.ethz.ch/pipermail/bioc-devel/2020-March/016365.html

                   Changes in version 1.21.10                       
  

BUG FIXES

• Add crop = NULL to all template Rmarkdown files. Drop magick as a depencency since cropping is not used on the reports (as done through BiocStyle by default). This is again related to responding to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html.

                   Changes in version 1.21.9                        
  

BUG FIXES

• Ran another test in preparation for https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html after the test in version 1.21.8 failed. The code will now be run in the example of derfinderReport() instead of the vignette.

                   Changes in version 1.21.8                        
  

BUG FIXES

• In an attempt to fix the bug I reported at https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html and in preparation to reply to this thread, I’m experimenting with suggesting that magick is installed, at which point BiocStyle will try to crop. Another option might be to use crop = NULL on all Rmd files.

                   Changes in version 1.21.5                        
  

BUG FIXES

• The example in renderReport() was failing because the first time the function was called, it ran derfinder::makeGenomicState() which in turn uses GenomicFeatures::isActiveSeq(). derfinder version 1.21.5 fixed this bug and is thus required by regionReport now.

                   Changes in version 1.21.4                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Add links to the example reports created when deploying the documentation website with pkgdown::deploy_to_branch(). This eliminates the need for the vignetttes/Makefile and the fake vignettes. It should also avoid confusing pkgdown.

                   Changes in version 1.21.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://leekgroup.github.io/derfinderPlot/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

                   Changes in version 1.21.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Now use GenomeIndoDb::getChromInfoFromUCSC() instead of data(hg19Ideogram, package = ‘biovizBase’) to get the hg19 chromosome lengths.

regutools

                   Changes in version 0.99.14                       

SIGNIFICANT USER-VISIBLE CHANGES

• Now connect_database() as a bfc parameter instead of path.

                   Changes in version 0.99.13                       
  

SIGNIFICANT USER-VISIBLE CHANGES

• Now connect_database() uses BiocFileCache::BiocFileCache() and BiocFileCache::bfcrpath() to download the database from Dropbox when it’s not available from AnnotationHub::query() and caches the file so you don’t have to re-download it multiple times.

                   Changes in version 0.99.12                       
  

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://comunidadbioinfo.github.io/regutools/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

                   Changes in version 0.99.11                       
  

BUG FIXES

• Manual adjustment for lines > 80 chr in parameters description.

                   Changes in version 0.99.10                       
  

BUG FIXES

• Bump Version to run R CMD check

                   Changes in version 0.99.9                        
  

BUG FIXES

• Add a suggested biocView Transcription.

                   Changes in version 0.99.8                        
  

BUG FIXES

• Change biocViews from AnnotationData to Software

                   Changes in version 0.99.7                        
  

BUG FIXES

• Fix a bug in pkgdown that is currently resolved by Rscript -e ‘remotes::install_github(“r-lib/pkgdown#1276”)’. Details at https://github.com/r-lib/pkgdown/pull/1276 and related issues.

                   Changes in version 0.99.6                        
  

BUG FIXES

• Manual adjust for some lines > 80 characters

                   Changes in version 0.99.5                        
  

BUG FIXES

• Reindent lines and try line-wrapping for lines > 80 characters

                   Changes in version 0.99.4                        
  

NEW FEATURES

• Added a NEWS.md file to track changes to the package.

                   Changes in version 0.99.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• DESCRIPTION file now contains an article-like summary in the field regutools package Description. - DESCRIPTION was updated to show only one maintainer as required by http://bioconductor.org/developers/package-guidelines/#description

BUG FIXES

• Fix a bug in the function get_regulatory_network() related with Cytoscape conection.

                   Changes in version 0.99.2                        
  

SIGNIFICANT CHANGES

• Removed the regutools.Rproj file (you can still have it, but it’s not version controlled). - Bump R depends to 4.0 as required by BiocCheck. We’ll see if it breaks.

                   Changes in version 0.99.1                        
  

BUG FIXES

• Address as many errors, warnings and notes as possible from http://bioconductor.org/spb_reports/regutools_buildreport_20200302121040.html#malbec2_check_anchor. For the Windows error, it’s likely related to mode = “w” versus mode = “wb” for utils::download.file() as in https://github.com/LieberInstitute/spatialLIBD/commit/7ac24dc72cc75e42c9af8382c661517f4a64f08d.

                   Changes in version 0.99.0                        
  

NEW FEATURES

• Submitted to Bioconductor

rfaRm

             Changes in version 0.99.0 (2020-04-08)                 

• Submitted to Bioconductor

rGREAT

                   Changes in version 1.19.1                        

• add ‘tsv’ option in getEnrichmentTables()

rhdf5

                   Changes in version 2.32.0                        

NEW FEATURES

• Added support for writing and reading datasets using the R ‘raw’ datatype.

• HDF5 functions H5Tset_strbuf and H5Tget_strbuf are now exposed.

CHANGES

• R ‘logical’ values are now stored as 8-bit integers rather than 32-bit integers. (Response to suggestions in https://github.com/grimbough/rhdf5/pull/55)

• Default compression level is 6 for all functions, rather than a mix of 6 or 7 in different places.

• Character vectors writen as HDF5 strings are now null padded by default, rather than null terminated. (Response to https://github.com/grimbough/rhdf5/pull/50)

BUG FIXES

• Writing data.frames with more than one factor column no longer leads to memory explosion.

• Bug in h5ls() which could lead to failure in printing the dataset dimensions has been fixed.

• Patched bug in h5write which left an unclosed HDF5 datatype object when writing strings.

rhdf5filters

                   Changes in version 0.99.0                        

• Initial submission to Bioconductor

ribor

                   Changes in version 0.99.7                        

• All parameter names are in singular version. The parameters region and experiment are the parameter names for all applicable functions. The experiment parameter can still take in a list of multiple experiments and the region parameter can as well except for the case of getting the length distribution.

• Validator and accessor methods have been added. Use ?Ribo for more details on the available methods.

• The return types for the reader functions are currently either S4Vectors DataFrame or the R native data.frame, depending on the presence of the added compact parameter.

• Documentation has been added to be more thorough.

                   Changes in version 0.99.0                        
  

• Submitted to Bioconductor

ribosomeProfilingQC

                   Changes in version 0.99.91                       

• change Y-axis lable from Frequence to Frequency for plot Distance2Codon. - update vignette.

                   Changes in version 0.99.9                        
  

• reset the test_estimatePsite.

                   Changes in version 0.99.8                        
  

• decrease the testing time.

                   Changes in version 0.99.6                        
  

• fix the warning missing link of plot in plotTE.

                   Changes in version 0.99.5                        
  

• update ggBar function to accept more colors. - update readsEndPlot function with shift parameter. - update plotDistance2Codon function with a range of plot window - add codonUsage function.

                   Changes in version 0.99.4                        
  

• update the description in DESCRIPTION. - update help files.

                   Changes in version 0.99.3                        
  

• change the link from AtomicList to AtomicList-class and RUVs-methods to RUVs. - shorter lines < 80 characters. - spead up coverageDepth

                   Changes in version 0.99.2                        
  

• remove .DS_Store

                   Changes in version 0.99.1                        
  

• decrease the size of the package - simplify and add parameter anchor for the estimatePsite function. - add parameter normByLibSize for function translationalEfficiency - add more test files. - update documentations.

                   Changes in version 0.99.0                        
  

• Submit to Bioconductor.

                    Changes in version 0.0.6                        
  

• Remove sapply.

                    Changes in version 0.0.1                        
  

• Create the package.

RMassBank

                   Changes in version 2.15.3                        

• Fix an issue if saved InfoLists have missing columns

                   Changes in version 2.15.2                        
  

• Merge PR by Adelene Lai to add CompTox information

• Merge PR by Hendrik Treutler to 1) add more CH$NAME fields and 2) more Adducts and 3) Selenium

RNAAgeCalc

             Changes in version 0.99.1 (2019-08-30)                 

• Package created

RNAdecay

                    Changes in version 1.6.1                        

• Updates for Bioconductor 3.11: new function: hl_plot, fixed decay_plot bugs, rewrote cols function.

RNAmodR

             Changes in version 1.1.1 (2019-11-10)                  

• added missing implementation for compare and subset functions

ropls

                   Changes in version 1.19.16                       

INTERNAL MODIFICATION

• ‘.header’ function: ‘class(x) == ‘ removed from code to take into account the R 4.0 changes

                   Changes in version 1.19.14                       
  

INTERNAL MODIFICATION

• ‘strF’ function: use of is.array instead of is.matrix to take into account the R 4.0 changes

                   Changes in version 1.19.12                       
  

INTERNAL MODIFICATION

• ‘strF’ function: replacement by ‘is(x, )’: cont’d

                   Changes in version 1.19.10                       
  

INTERNAL MODIFICATION

• ‘strF’ function: ‘class(x) ==’ replaced by ‘is(x, )’ as required by R/Bioconductor

                   Changes in version 1.19.8                        
  

NEW FEATURE

• ‘view’ method: ‘standardizeL’ argument for the standardization of column values for display

                   Changes in version 1.19.6                        
  

BUG FIXED

• ‘view’ method: ExpressionSet with empty metadata

                   Changes in version 1.19.4                        
  

NEW FEATURE

• ‘view’ method: plot extended to data.frames and ExpressionSet

                   Changes in version 1.19.2                        
  

BUG FIXED

• ‘view’ method: in case the matrix has no row nor column names

ROSeq

                   Changes in version 1.99.01                       

— no bug, but removed extra files from man folder

                   Changes in version 0.99.23                       

— updated authors names

                   Changes in version 0.99.22                       

— no bug, but removed some part of code that was not necessary

                   Changes in version 0.99.21                       

— no bug, but corrected package version format

                   Changes in version 0.99.9                        

— no bug

                   Changes in version 0.99.8                        

— no bug, but version dependancy changed 3.6 to 4.0

                   Changes in version 0.99.7                        

— error was removed

                   Changes in version 0.99.6                        

— got one error, now is removed

                   Changes in version 0.99.5                        

— no bug, but removed notes

                   Changes in version 0.99.4                        

— no bug, but version dependancy changed 3.6 to 4.0

                   Changes in version 0.99.3                        

Bugfixes

• no bug, but i corrected all previous issues of 11 Dec as shown below - corrected i have listed all program in documentation - changed according to <- or = - used importFrom methods of the package instead of the whole package. - print removed from code - used seq_len() this time instead of : - no need for message required - used vapply function this time - getd2logAdbda<-getd2logAdb2<-getd2logAdadb<-getd2logAda2 issue solved

• last issue of BiocManager::install(‘ROSeq’) solved

                   Changes in version 0.99.2                        
  

Bugfixes

• no bug

                   Changes in version 0.99.1                        
  
                    Changes in version 0.0.1                        
  

Bugfixes

• removing src folder

                 Changes in version 0.0.0.9000                      
  

setup

• added NEWS.md creation

RProtoBufLib

                    Changes in version 2.0.0                        

• update protobuf to 3.10

                   Changes in version 1.99.0                        
  

• bundle the protobuf c++ library and expose its headers and static libraries

rpx

                    Changes in version 1.23                         

Changes in version 1.23.1

• Define modifiable rpx_fix_issue_5 <2019-11-26 Tue>

Changes in version 1.23.0

• New devel version

rrvgo

                   Changes in version 0.99.1                        

• First release to Bioconductor

Rsamtools

                     Changes in version 2.4                         

BUG FIXES

• (v 2.3.2; from v 2.2.2) Correctly handle ‘*’ (‘unknown’) RNAME during paired-end processing. See https://github.com/Bioconductor/Rsamtools/issues/16.

• (v 2.3.5) Fix regression introduced by v 2.3.2

NEW FEATURES

• (v 2.3.1) Don’t require BAM files to have @SQ lines; allows parsing PacBio ‘unaligned’ BAM files. (https://github.com/Bioconductor/Rsamtools/issues/15 ; jayoung)

rScudo

                    Changes in version 1.3.1                        

USER VISIBLE CHANGES

• Updated vignette and converted it to html

Rsubread

                    Changes in version 2.2.0                        

• Improve cellCounts() on the identification of cell barcodes arising from ambient RNAs.

rSWeeP

            Changes in version 0.99.12 (2020-02-08)                 

• 2000+ sequences multifasta error removed

             Changes in version 0.99.7 (2020-01-21)                 
  

• Warning removed

             Changes in version 0.99.6 (2020-01-21)                 
  

• Error removed

             Changes in version 0.99.5 (2020-01-21)                 
  

• An even bigger FASTA has been used in the “Quick Start” section

             Changes in version 0.99.4 (2020-01-21)                 
  

• The package no longer relies on seqinr, now operates only with Biostrings functions and variables

• The Title and the Description have been updated to be more precise in describing the package.

• Despcritional comments have been added to all codes.

• The sWeeP functions now accept AAStringset as well file names as a valid entry

• The sWeeP function now uses an S4 Generic and S4 methods

• The user input variable baseMatrix has now a validating step on the code

• The sWeeP function now uses Biostrings::readAAStringSet for FASTA input.

• All functions now only use message(…) to communicate with users.

• All 1:length(…) instances have been replaced with seq_len

• On all codes, the function tidy_source() from the formatR package has been used to standardizing code formating.

• All operations that do not affect have to the package working been removed.

• Some functions and variables naming has been changed aiming to follow the lowerCamelCase convention (the sWeeP function still as it’s, due it is the method initials)

• aa2int() has been replaced by a vector inside the aa2num2()

• The data set datastring has been removed.

• fas2mat receives now an AAStringSet as entry

• Instead of reading the R object datastring and writing it as a FASTA file, a FASTA file has been included directly in inst/extdata/

• A bigger FASTA has been used in the “Quick Start” section

• All non-R package source files have been removed

             Changes in version 0.99.0 (2019-05-15)                 
  

• Submitted to Bioconductor

RTCA

                 Changes in version 2009-07-13                      

• combineRTCA(list): Additional column is renamed into Plate. The vlues is evaluated from list item names. When the list has no name, an integer index beginning from 1 is used. Special attentions to list partially with names is noted in the documentation.

• parseRTCA(file, dec=”.”,phenoData, skipWell,…): Example is added in the documentation how to import pre-configured phenoData. Details section in the documentation is re-written to describe the process of parsing.

• RTCA-class: Experiment ID added to RTCA class

• Makefile: add Makefile to simplify common tasks like check and install

• plotGridEffect: takes ‘column’ instead of ‘col’ as mode parameter, and renders the mode as the title of the legend. Documentation updated.

• plotRTCA: is removed from the package and is substituted by the plot function.

RTCGAToolbox

                   Changes in version 2.18.0                        

New features

• Warning for Windows users added when file paths are too long - getGISTICPeaks now requires a FirehoseGISTIC data object obtained from getFirehoseData

Bug fixes and minor improvements

• Consolidate GISTIC data download methods in getFirehoseData and getGISTICPeaks - Increase robustness of internal helper functions that work with strands - ‘TCGA’ sample column identification is less strict

RUVcorr

                   Changes in version 1.19.0                        

• Changed class calling.

• New vignette.

rWikiPathways

                    Changes in version 1.8.0                        

• Replaced RJSONIO with rjson

• Replaced all but one sapply() with vapply()

• Deprecated getColoredPathway

• New features - Upgraded findPathwaysByXXX, listPathways and getPathwayInfo functions to return dataframes - Upgraded findPathwaysByLiterature to present literature fields

• Doc fixes - Updated tests and vignettes using dataframes

S4Vectors

                   Changes in version 0.26.0                        

NEW FEATURES

• Add TransposedDataFrame objects.

• Add make_zero_col_DFrame() for constructing a zero-column DFrame object. Intended for developers to use in other packages and typically not needed by the end user.

• Add internal generic makeNakedCharacterMatrixForDisplay() to facilitate implementation of show() methods. Also add cbind_mcols_for_display() helper for use within makeNakedCharacterMatrixForDisplay() methods.

SIGNIFICANT USER-VISIBLE CHANGES

• Rename parallelSlotNames() internal generic -> vertical_slot_names(). Also add new horizontal_slot_names() internal generic (no methods yet).

BUG FIXES

• Fix bug causing segfault in C function ‘select_hits()’ when ‘nodup’ is TRUE.

SAIGEgds

                    Changes in version 1.2.0                        

• seqAssocGLMM_SPA() can save to a RDS file

                    Changes in version 1.0.2                        
  

• fix an issue when there is no covariate in the formula (e.g., y ~ 1)

                    Changes in version 1.0.1                        
  

• add a new option for the threshold of missing variant to seqAssocGLMM_SPA()

• change the output column ‘AC.alt’ to ‘mac’ in seqAssocGLMM_SPA()

• retry model fitting at least 10 times if matrix is singular or not positive definite, or large variance is observed

sarks

             Changes in version 0.99.0 (2020-02-14)                 

• Submitted to Bioconductor

scater

                   Changes in version 1.16.0                        

• Added coldata_merge= argument to aggregateAcrossCells() for custom column metadata aggregation. Also include averaged reduced dimension results for each group.

• Added label_format= argument to plotReducedDim() for greater control over the axis labels.

• Added geometric= argument to librarySizeFactors() to compute size factors with a geometric mean.

• Added the runMultiUMAP() function to perform a combined UMAP on multiple feature sets.

• Added the medianSizeFactors() function to perform a DESeq2-like size factor calculation.

• Modified isOutlier() so that min_diff= now acts on the log2 scale when log=TRUE. Added share_medians=, share_mads= and share_missing= options for sharing information across batches.

• Exposed various developer utilities for downstream packages.

• Modified sumCountsAcrossCells() to always return a SummarizedExperiment object, regardless of the class of ids. Return the number of cells used for summation in the colData.

• Restored capability to create a data.frame from a SCE with makePerCellDF() and makePerFeatureDF().

• Added ggcells() and ggfeatures() for convenient creation of ggplot objects from a SCE.

scClassify

                   Changes in version 0.99.3                        

• Improve coding format - sapply changed to vapply - Add examples - Improve vignettes

schex

                    Changes in version 1.1.4                        

• Option to remove NAs for plot_hexbin_meta*.

                    Changes in version 1.1.3                        
  

• Updated the vignettes and example code to incorporate changes. - Added bivariate plotting feature.

                    Changes in version 1.1.2                        
  

• Changes to vignettes to comply with changes in Seurat

                    Changes in version 1.1.1                        
  

• Deprecated plot_hexbin_gene. - Updated plot_hexbin_feature to use all features, including genes. - Introduced plot_hexbin_fc for fold change visualization. - Introduced plot_hexbin_meta_plus and plot_hexbin_feature_plus to plot cluster outlines. - Introduced plot_hexbin_meta_shiny, plot_hexbin_feature_shiny and plot_hexbin_density_shiny for interactive visualization. - Changed internal structure. - Updated vignettes. - Included two new vignettes. - New README.

SCOPE

                   Changes in version 0.99.13                       

• Integrate mouse genome and update plot_iCN()

                   Changes in version 0.99.12                       
  

• add algorithms with shared clonal memberships

                   Changes in version 0.99.11                       
  

• get_gc() dontrun

                   Changes in version 0.99.8                        
  

• minor edit

                   Changes in version 0.99.7                        
  

• second-round revision

                   Changes in version 0.99.6                        
  

• first-round revision

                   Changes in version 0.99.5                        
  

• Enable user-define bin length and offer SoSplot

                   Changes in version 0.99.4                        
  

• Add .bed file for hg38

                   Changes in version 0.99.3                        
  

• Test if SCOPE is linked to WGSmapp

                   Changes in version 0.99.2                        
  

• Bump new version to trigger a build

                   Changes in version 0.99.1                        
  

• Add session_info() to the vignette

                   Changes in version 0.99.0                        
  

• SCOPE getting ready for submission to Bioc

scPCA

             Changes in version 1.1.14 (2020-04-26)                 

• Fixing broken link in an internal function documentation page.

             Changes in version 1.1.12 (2020-04-21)                 
  

• Updated citations - Fixed typos in documentation

             Changes in version 1.1.11 (2020-02-02)                 
  

• Added more SPCA algorithm options - SPCA via variable projection - Randomized SPCA via variable projection - New vignette section comparing performance of SPCA algorithms - Improvements to code coverage

             Changes in version 1.1.5 (2020-01-18)                  
  

• Fixed issue with matrix normalization - Misc. big fixes - Improvements to code coverage

             Changes in version 1.1.2 (2020-01-08)                  
  

• Added hierarchical clustering options for clustering based cross-validation

scPipe

             Changes in version 1.9.4 (2020-04-06)                  

• Changed hashmap package calls to hash package as hashmap is no longer on CRAN.

             Changes in version 1.9.1 (2019-12-23)                  
  

• Changed instances of deprecated plotQC() to plotHighestExprs()

scran

                   Changes in version 1.16.0                        

• Added the quickSubCluster() function for convenient subclustering.

• Added the bootstrapCluster() function to convenient bootstrapping of cluster stability.

• Added the coassignProb() function to compute coassignment probabilities of alternative groupings.

• combineMarkers() and findMarkers() report a summary effect size for each cluster.

• Added the multiMarkerStats() function to combine statistics from multiple findMarkers() calls.

• Added the clusterPurity() function to evaluate cluster purity as a quality measure.

• Added the pseudoBulkDGE() function to easily and safely perform pseudo-bulk DE analyses. Also added the decideTestsPerLabel() and summarizeTestsPerLabel() utilities.

• Added the clusterSNNGraph() and clusterKNNGraph() wrapper functions for easier graph-based clustering. Provided a k-means pre-clustering option to handle large datasets.

scry

                     Changes in version 1.0                         

• Initial release of the scry package for analysis of high-dimensional data consisting of small counts (such as single-cell RNA-seq). Features included in this release:

• Feature selection with deviance - Dimension reduction with GLM-PCA
• Approximate GLM-PCA using Pearson and deviance residuals from a null model. - Optional adjustment for categorical batch effects for all methods. - Support for SingleCellExperiment and SummarizedExperiment objects - Support for matrix and sparse Matrix objects.

scTensor

                    Changes in version 1.4.0                        

• verbose parameter was added in cellCellRank() and cellCellDecomp()

• set.seed(1234) was added in example and vignette

• .cellCellDecomp.CabelloAguilar() and .cellCellDecomp.Halpern() were added

• The num.iter 300　of NTD was changed to 30

• schex package was imported for visualing all the two dimensional gene plots

• The rule of cellCellRanks() based on the singular value of SVD was changed to a reconstruction error based rule, using NMF with matricised tensor in each mode

• The CCI-tensor is normalized in each frontral slice so that the total value is 1 (.frontal.normalization)

                    Changes in version 1.2.1                        
  

• Some bugs were fixed

scTHI

             Changes in version 0.99.6 (2020-03-02)                 

• Submitted to Bioconductor

SDAMS

                    Changes in version 1.7.1                        

• add reference.

selectKSigs

                   Changes in version 0.99.5                        

• Remove git track src-i386 and src-x64.

                   Changes in version 0.99.4                        
  

• Address all error messages.

                   Changes in version 0.99.3                        
  

• Address all comments from the Bioconductor reviewer.

                   Changes in version 0.99.2                        
  

• Remove selectKSigs.Rproj.

                   Changes in version 0.99.1                        
  

• Submitted to Bioconductor.

SeqArray

                   Changes in version 1.28.0                        

NEW FEATURES

• new function seqUnitSlidingWindows()

• new function seqUnitApply()

• new variable “$variant_index”, “$sample_index” in SeqGetData(), seqBlockApply() and seqUnitApply() to get the indices of selected variants

• new arguments ‘.padNA’ and ‘.envir’ in seqGetData()

• new functions seqSetFilterAnnotID() and seqGDS2BED()

• multicore function in seqBED2GDS(, parallel=)

• new package-wide option options(seqarray.nofork=TRUE) to disable forking

• new option ‘minor’ in seqAlleleFreq() and seqAlleleCount()

• new option ‘verbose’ in seqMissing(), seqAlleleFreq() and seqAlleleCount(); ‘.progress’ is deprecated, but still can be used for compatiblity

• seqAlleleFreq() and seqAlleleCount() work on ‘annotation/format/DS’, if ‘genotype/data’ is not available

UTILITIES

• seqAddValue() adds vectors, matrices and data frame to “annotation/info”

• seqBED2GDS() allows a single file name without the extended file names (.bed, .fam, .bim)

• allele flip in seqBED2GDS() to allow major allele to be reference

• rewrite seqGetData() for faster loading

• significantly improve seqBlockApply() on ‘annotation/info/VARIABLE’ (https://github.com/zhengxwen/SeqArray/issues/59)

• add a S3 method print.SeqVCFHeaderClass() for seqVCF_Header()

• new option ‘.tolist’ in seqGetData(), seqBlockApply() and seqUnitApply()

• String “.” in a VCF file are converted to a blank string (missing value) in seqVCF2GDS()

• add a class name ‘SeqVarDataList’ to the returned ‘list(length, data)’ from seqGetData()

• new option seqMissing(, per.variant=NA)

• add comment.char="" to seqBED2GDS()

                   Changes in version 1.26.2                        
  

NEW FEATURES

• multiple variable names are allowed in seqGetData(, var.name=)

BUG FIXES

• fix seqGetData(, "genotype", .useraw=NA) (https://github.com/zhengxwen/SeqArray/issues/58)

                   Changes in version 1.26.1                        
  

BUG FIXES

• fails to correctly select duplicate indices in seqSetFilter(f, variant.sel=)

SeqVarTools

                   Changes in version 1.25.1                        

• Bug fix in minorAlleleCount when all samples have the same sex.

sevenbridges

                   Changes in version 1.17.1                        

Bug Fixes

• Fix build issues in R 4.0.0, in which the the default value for stringsAsFactors is changed to FALSE. Updated the affected data.frame() calls which rely on the default automatic vector expansion behavior with explicit stringsAsFactors = TRUE.

SharedObject

                    Changes in version 1.1.6                        

• Add memory check on Linix system

                    Changes in version 1.1.1                        
  

• Refactoring code

• Add supports for package developer at C++, R levels

signatureSearch

             Changes in version 1.0.6 (2020-04-19)                  

• Supported searching refdb parallelly by using multiple cores on a single machine

             Changes in version 1.0.5 (2020-04-10)                  
  

• Fix bug: fixed null issue and throw warning messages when up or down gene sets share zero identifiers with refdb for gess_lincs method.

             Changes in version 1.0.4 (2020-04-02)                  
  

• Added instructions for GESS batch queries in vignette - Added runWF function to run entire GESS/FEA workflow

             Changes in version 1.0.3 (2020-02-07)                  
  

• Supported converting feaResult object to enrichResult object in the clusterProfiler package so that the plotting functionalities in the latter package such as dotplots and gene-concept networks could be applied to the FEA enrichment results - Supported searching against subset of refdb (subsetted specific columns (treatments) in the refdb (e.g. lincs)) for GESS methods - Updated comp_fea_res function to reduce number of characters in description - Added functions to draw different types of query GESs from refdb - Added deprof2subexpr function to get a subset of gene expression values from a differential expression profile

             Changes in version 1.0.2 (2020-01-21)                  
  

• Fix bug: the enrichment results from DSEA methods and some of TSEA methods were added an aditional ‘ont’ column where the GO itmes were subsetted to the selected ontology

             Changes in version 1.0.1 (2019-11-10)                  
  

• Support windows by not depending gCMAP package - Deal with HDF5 files with functions in HDF5Array package

signeR

                   Changes in version 1.13.1                        

• fix issue with pseudo-variants on vcf

SimFFPE

             Changes in version 0.99.0 (2019-12-12)                 

• Submitted to Bioconductor

SingleCellExperiment

                   Changes in version 1.10.0                        

• Removed deprecated modes for getting and setting reducedDims.

SingleR

                    Changes in version 1.2.0                        

• Added support for consolidating labels from multiple references via combineResults().

• Added mappings to standardized Cell Ontology terms in all *Data() functions.

• Changed the name of the labels input of plotScoreDistribution() to labels.use for consistency across functions.

• Fixed a label from adipocytes to astrocytes in BlueprintEncodeData().

• Removed umlauts from labels (e.g., naive) in NovershternHematopoieticData() to avoid problems with Windows.

• Perform PCA before clustering in aggregateReference() for speed and memory efficiency.

• Modified genes=”all” behavior in trainSingleR() to report DE-based markers for fine-tuning only.

singscore

                    Changes in version 1.8.0                        

• implemented a novel approach to scoring that uses measurements from panel-based tests such as RT-qPCR and nanostring - implemented a function that returns a set of stable genes we have identified in carcinomas and in blood - fixed bugs in the multiScore function that produced errors when scoring a single sample - fixed bugs in the generateNull function that produced errors when assessing a single geneset - fixed bugs in the vignette

sitePath

                    Changes in version 1.2.2                        

• Bug fix: infinity loop might occur when using ‘fixationSites’ or ‘multiFixatoinSites’ caused by internal function. There’s no solution for version 1.2.x, so choices are given to possibly avoid it.

• Bug fix: malfunctional ‘setSiteNumbering’.

                    Changes in version 1.2.1                        
  

• Bug fix: plot warning caused by ‘tab’ character

• Bug fix: bad design causing ‘multiFixationSites’ extremely slow

• Bug fix: ‘fixationSites’ gives replicated tips when combined

snapcount

             Changes in version 0.99.0 (2019-09-17)                 

• Submitted to Bioconductor

SNPRelate

                   Changes in version 1.22.0                        

• ‘allow.fork=TRUE’ is the default in snpgdsOpen() since v1.21.2

• add print.snpgdsPCAClass, print.snpgdsEigMixClass, print.snpgdsPCASNPLoadingClass, print, snpgdsEigMixSNPLoadingClass, print.snpgdsIBDClass, print.snpgdsDissClass, print.snpgdsIBSClass

• fix a Win32 compiler issue with gcc-4.9

• update snpgdsBED2GDS() with comment.char=””

                   Changes in version 1.20.1                        
  

• Bug fix: eigenvalues and TraceXTX are correctly calculated in snpgdsPCA(, algorithm="randomized")

sojourner

                    Changes in version 1.1.4                        

• Modified readme file for new user.

                    Changes in version 1.1.3                        
  

• bug fixes for Bioc3.11

                    Changes in version 1.1.2                        
  

• SDMTools dependency removed

                    Changes in version 1.1.1                        
  

• rowr dependency removed.

                    Changes in version 1.1.0                        
  

• BioC3.10 release.

sparseMatrixStats

             Changes in version 0.0.99 (2020-04-03)                 

• Submitted to Bioconductor

SpatialCPie

                     Changes in version 1.3                         

• (1.3.4) Fixed type error when resolutions only have one cluster

• (1.3.3) Fixed vignette field name

• (1.3.2) Renamed cluster tree to cluster graph

splatter

             Changes in version 1.12.0 (2020-04-20)                 

• Add checks for cycles in the Splat path.from parameter.

• Use alternative algorithm if fitting dropout fails in splatEstimate.

• Adjust paths example in vignette.

• Replace defunct functions in vignettes.

• Minor fixes for compatibility with updates to other packages.

spqn

                    Changes in version 0.99                         

• Submission to Bioconductor. This package implements the SpQN method for normalizing correlation matrices, as described in Wang, Hicks and Hansen (2020) bioRxiv.

SSPA

                   Changes in version 2.27.1                        

• convert Rnw vignette to Rmd

• fixed R_CHECK_LENGTH_1_LOGIC2

statTarget

                     Changes in version 2.0                         

NEW FEATURES

• New GUI o Mouse Hover for help information o .log file

• New Signal correction o Combat for QC-free Signal correction o QC-RFSC methods for metabolomics and proteomics data

• New feature slection o Random Forest and the Permutation based variable importance measures o new MDSplot for Random Forest o P-value based importance plot

• New data preprocessing o PQN/SUM/none normalization o center/none Scaling method

                   Changes in version 1.17.3                        
  

• shiftCor-coCV was added as the cutoff value (0-100) of CV for controlling the number of features.

• To fixed bugs for skiping the roc analysis once the number of samples in any groups was less than 5.

                   Changes in version 1.17.2                        
  

• Check and remove the missing values in pvalues for volcanoplot functions

struct

                   Changes in version 0.99.10                       

• update vignettes

• update documentation

• add ‘signature’ input to struct_obj_method

                   Changes in version 0.99.9                        
  

• subsetting of iterators with a single model now converts to a model sequence with 1 step

                   Changes in version 0.99.8                        
  

• documentation changes for Bioconductor checks

                   Changes in version 0.99.7                        
  

• fixed broken is_valid for .outputs

• minor documentation updates

                   Changes in version 0.99.6                        
  

• .params and.outputs inherited correctly

• fix some documentation issues

                   Changes in version 0.99.5                        
  

• added as.DatasetExperiment for converting SummarizedExperiment objects

             Changes in version 0.99.4 (2020-02-04)                 
  

• Set initial value for entity on creation if not provided

• Rename enum ‘list’ to ‘allowed’

             Changes in version 0.99.3 (2020-02-03)                 
  

• Improved use of class constructors

                   Changes in version 0.99.2                        
  

• incremental changes in response to bioconductor feedback

                   Changes in version 0.99.1                        
  

• incremental changes in response to bioconductor feedback

                   Changes in version 0.99.0                        
  

• Bioconductor submission

                    Changes in version 0.4.1                        
  

• Final working release before bioconductor submission

             Changes in version 0.2.0 (2019-07-25)                  
  

• Introduction of seq_out slot for more flexible workflows (currently method objects only)

Structstrings

             Changes in version 1.3.1 (2019-12-01)                  

• Display Dot Bracket sequences in color

structToolbox

                   Changes in version 0.99.10                       

• add Metabolmics BiocView

• fix missing sections at end of vignette

                   Changes in version 0.99.9                        
  

• add proteomics vignette

• add mean_of_medians

• merge all vignettes

• fix bug in kfold_xval_grid

                   Changes in version 0.99.8                        
  

• added stratified splitting (stratified_split)

• added Gastric Cancer vignette

• add AUC metric

• add predicted and ROC plots for PLSDA

                   Changes in version 0.99.7                        
  

• minor documentation updates

                   Changes in version 0.99.6                        
  

• fix issues using class() due to changes in R 4.0.0

                   Changes in version 0.99.5                        
  

• fix dimnames mismatch for knn-impute

• add additional vignettes

                   Changes in version 0.99.4                        
  

• Add SVM, nroot transform, constant sum norm

• Add funtionality to autoscaling

• Fix some issues with permutation testing of model sequences

• Add option to impute by samples to knn

• Add custom feature labels option to pca loadings

                   Changes in version 0.99.3                        
  

• Fix dimnames mismatch errors

• Updated struct depency to 0.99.5

                   Changes in version 0.99.2                        
  

• renamed some charts containing .’s to use underscores

• renamed sbcms dataset to MTBLS79

                   Changes in version 0.99.1                        
  

• minor updates to pass Bioconductor checks

                   Changes in version 0.99.0                        
  

• use new struct v0.99.4 class constructor functions

                    Changes in version 0.8.4                        
  

• Final working version befor bioconductor updates

             Changes in version 0.4.0 (2019-07-25)                  
  

• Minor bug fixes

• Added tsne method

• Added sbcms dataset

• Added methods related to signal/batch correction

SubCellBarCode

             Changes in version 1.2.6 (2020-04-08)                  

• Changed the NEWS.md file to track changes to the package.

• Fixed bug.

SummarizedExperiment

                   Changes in version 1.18.0                        

NEW FEATURES

• SummarizedExperiment objects with assays of > 4 dimensions are now fully supported.

SIGNIFICANT USER-VISIBLE CHANGES

• By default the assays() and assay() setters now reject inconsistent dimnames. By default the dimnames on the supplied assay(s) must be identical to the dimnames on the SummarizedExperiment object. The user now must use ‘withDimnames=FALSE’ if it’s not the case or they get an error. This is for symmetry with the behavior of the assays() and assay() getters (see issue #35). Unfortunately this change is likely to break existing code but at least the fix is easy.

• dimnames() now returns NULL instead of list(NULL, NULL) on a SummarizedExperiment object with no dimnames. This is consistent with matrix objects.

• Swap positions of arguments ‘…’ and ‘withDimnames’ in assays() setter and getter. So now it’s: assays(x, withDimnames=TRUE, …) assays(x, withDimnames=TRUE, …) <- value

• Add ‘withDimnames’ argument to the assay() getter/setter. So now it’s: assay(x, i, withDimnames=TRUE, …) assay(x, i, withDimnames=TRUE, …) <- value Note that before this change, the user was able to explicitly set ‘withDimnames’ when calling assay() but since this was not a formal argument it was forwarded to assays() via the ellipsis. Having it as a formal argument makes it easier to discover and allows tab completion.

SWATH2stats

                   Changes in version 1.17.5                        

update

• .Rmd vignettes: remove tinytex option

                   Changes in version 1.17.4                        
  

update

• convert_protein_ids: Also count empty strings as NA and count unique non-mapped identifiers.

                   Changes in version 1.17.3                        
  

update

• plot_correlation_between_samples.R, plot_variation.R, plot_variation_vs_total.R: improve plots and do theme_bw

                   Changes in version 1.17.2                        
  

NEW FEATURES

• filter_on_min_peptides.R: add ability to deal with PeptideSequence column

• filter_on_max_peptides.R: add ability to deal with PeptideSequence column

                   Changes in version 1.17.1                        
  

UPDATE

• convert_protein_ids: count unique non-mapped IDs.

                   Changes in version 1.17.0                        
  

NEW FEATURES

• SWATH2stats in BioC 3.11 development release

SynExtend

                   Changes in version 0.99.30                       

• Vignette and help files edited for clarity

                   Changes in version 0.99.1                        
  

• SynExtend submitted to Bioconductor - Added function gffToDataFrame
• Added function NucleotideOverlap - Added function PairSummaries

systemPipeR

• With the upgrades provided in this release, systemPipeR has become a much more generic data analysis workflow environment that is no longer limited to analyzing just NGS data. Now it can be efficiently used for data analysis tasks in many omics areas, including genomics, proteomics, metabolomics and drug discovery.
• A workflow control class (SYSargsList) has been added allowing users to manage multiple-step workflows from a single container. This way one can select and execute multiple workflow steps with standard R subsetting syntax, e.g. runWF[1:3].
• Various improvements have been added to systemPipeR’s new command-line interface including the recently introduced SYSargs2 class that supports the Common Workflow Language (CWL).
• Utilities have been added to visualize workflow designs and topologies with different graphical layouts.
• Improvements have been added to monitor the run status of workflows as well as better tracking of warning and error messages. This includes the generation of both scientific and technical status reports.

TAPseq

             Changes in version 0.99.0 (2020-02-21)                 

• Initial submission to Bioconductor

TargetSearch

                   Changes in version 1.44.0                        

NEW FEATURES

• The class tsRim allows subsetting by the [ operator. This makes possible to choose specific marker for plotting, eg, in checkRimLim.

• New function updateRI to update/correct/force the time of the RI markers. Just like the old function fixRI, but it also corrects CDF files.

BUG FIXES

• Make sure matrix dimensions are not dropped in NCDF extraction.

• Fix check warnings due to plot() being moved to base.

• Clean-up NAMESPACE

TBSignatureProfiler

                 Changes in version 0.0.0.9000                      

• Added a NEWS.md file to track changes to the package.

TCGAutils

                    Changes in version 1.8.0                        

New features

• README.md now includes a cheat sheet for reference - mergeColData and oncoPrintTCGA sections updated/included in the vignette

Minor changes and bug fixes

• translateBuild more robust to consistent inputs - translateBuild returns vector output instead of single string as before - makeSummarizedExperimentFromGISTIC now has a more open interface with … input to RTCGAToolbox::getGISTICPeaks - oncoPrintTCGA now uses seqlevels from input throughout

TOAST

                    Changes in version 1.1.1                        

• Add options for partial reference-free deconvolution.

tofsims

                    Changes in version 099.1                        

SIGNIFICANT USER-VISIBLE CHANGES

• changed function behvaiour in the whole package from call-by-ref to call-by value. Adjusted accordingly all examples and the vignette.

INTERNALS

• depends now on ProtGenerics from which it uses ‘mz’

• exchanged various print() with message()

topconfects

                    Changes in version 1.3.1                        

• Fix y axis labels on confects_plot

topdownr

                     Changes in version 1.9                         

• New version for Bioc 3.11 (devel)

Changes in version 1.9.4

• Fix unit tests that check for “matrix” class. (class(m) now returns c(“matrix”, “array”) in r-devel) [2019-12-17].

Changes in version 1.9.3

• Adapt analysis vignette to changed condition argument [2019-11-22].

Changes in version 1.9.2

• Set conditions=”ScanDescription” as new default for readTopDownFiles. The creation of FilterString IDs in the method files was deprecated since over a year. conditions=”FilterString” is still possible for backward-compatibility [2019-11-22]. - Fix error message handling in .validFilename and .translateThermoIdToScanId [2019-11-22].

Changes in version 1.9.1

• Remove defaultMs1Settings and defaultMs2Settings [2019-11-18]. - Fix .rbind for lists with mixed data.frame and DataFrame [2019-11-18].

TPP

                   Changes in version 3.15.1                        

• remove dependency to the sme package because it is not available any more on CRAN.

TPP2D

             Changes in version 1.3.0 (2020-04-17)                  

• Carry-over detection is not used anymore

• Bootstrapping is done based on resampling of alternative model residuals onto null model fits

• getFDR replaces computeFdr (now deprecated)

• option to moderate F is now available in function getFDR

trackViewer

                   Changes in version 1.23.5                        

• replace class function by is function.

                   Changes in version 1.23.4                        
  

• fix a issue of “EXPR must be a length 1 vector”.

                   Changes in version 1.23.3                        
  

• fix a issue of vignette when visit ebi proteins api.

                   Changes in version 1.23.2                        
  

• plot multiple genes in one track.

                   Changes in version 1.23.1                        
  

• add interactionData track.

tradeSeq

             Changes in version 1.1.07 (2020-02-27)                 

• added testing against fold change cut-off for all DE tests

• default cut-off for deciding the rank of the variance-covariance matrix changed in patternTest and earlyDETest. This can impact the results of these tests. To return to original behaviour, set eigenThresh=1e-8 argument.

transcriptR

                   Changes in version 1.15.6                        

• Updated NEWS file to track changes in the package.

                   Changes in version 1.15.5                        
  

• Modified vignette to replace Rclass and Rfunction sweave syntax with markdown syntax.

                   Changes in version 1.15.4                        
  

• Modified vignette to add images via knitr::include_graphics.

                   Changes in version 1.15.3                        
  

• Changed vignette output format to html_document.

                   Changes in version 1.15.2                        
  

• Reformatted author section in the vignette yaml header.

                   Changes in version 1.15.1                        
  

• Fixed bug in the predictStrand function caused by the new behaviour of the data.frame introduced in R 4.0. Have to manually set stringsAsFactors=TRUE.

TreeAndLeaf

                   Changes in version 0.99.0                        

• Submitted to Bioconductor [2019-12-16].

treeio

                   Changes in version 1.11.3                        

• change according to dplyr (v=1.0.0) (2020-04-09, Thu) - remove mutate_, rename_, select_ and group_by_ - remove data_frame for it was deprecated in tibble (v=3.0.0)

                   Changes in version 1.11.2                        
  

• update citation (2020-02-18, Tue) - phyloxml parser read.phyloxml (2019-12-05, Thu)

                   Changes in version 1.11.1                        
  

• support jplace version 1 (2019-11-25, Mon) - https://github.com/YuLab-SMU/treeio/pull/25 - offspring return integer(0) instead of throw error if input .node is a tip (2019-11-21, Thu)

tRNAdbImport

              Changes in version 1.5 (2020-02-05)                   

• import of RNA sequences now disregards the insertion character “_”

• added tRNAdb_reference and tRNAdb_pmid columns to output

tRNAscanImport

             Changes in version 1.7.3 (2020-01-21)                  

• fixed get.tRNAprecursor() function if length of flanking sequences was not equal

• fixed istRNAscanGRanges() not returing a boolean value on fail

• removed remove.LowerCase argument from import.tRNAscanAsGRanges() since it was redundant

tscR

             Changes in version 0.99.2 (2020-05-06)                 

• Reviewer’s Suggestions Fixed

TSRchitect

                   Changes in version 1.13.5                        

• Corrected line in loadTSSobj() that caused a build error in the Bioc devel branch (3.11).

                   Changes in version 1.13.4                        
  

• Added feature to writeTSS() that generates two separate bedgraph files (plus and minus) instead of one.

                   Changes in version 1.13.3                        
  

• Updated documentation for loadTSSobj() for the sake of clarity.

                   Changes in version 1.13.2                        
  

• Corrected minor bugs in non-user-level functions detTSR() and detTSS()

• Various updates to Show-methods.R

                   Changes in version 1.13.1                        
  

• Version bump due to release of Bioconductor v. 3.10.

TVTB

             Changes in version 1.13.2 (2020-04-11)                 

Bug fix

• tSVE vignette output format set to HTML.

             Changes in version 1.13.1 (2020-03-26)                 
  

Bug fix

• parallelSlotNames() was renamed vertical_slot_names() in S4Vectors 0.25.14.

tximeta

                    Changes in version 1.6.0                        

• Added PLOS Computational Biology citation! :-)

• Added function splitSE to split one assay of a SummarizedExperiment into multiple assays, each containing features of a given type.

• Added a wrapper function makeDGEList() to simplify making a DGEList for use with edgeR. See vignette for example. + tximeta will now make use of EnsDb created and distributed on AnnotationHub, unless useHub=FALSE. Also, a new function retrieveDb() can be called on a SummarizedExperiment to retrieve the underlying TxDb or EnsDb. + tximeta can now use customMetaInfo argument to locate a custom metadata information file such as meta_info.json, which should contain a tage, index_seq_hash, with the SHA-256 hash value of the reference transcripts.

• Added markDuplicateTxps argument to add hasDuplicate and duplicates columns to rowData of SummarizedExperiment. One note is that, for efficiency, this argument and cleanDuplicateTxps will now share a duplicates CharacterList that is stored in the BiocFileCache, with the name dups-.... Therefore, if you have previously used cleanDuplicateTxps, you may need to bfcremove() any dups-... entries. Summarization to gene level will keep track of numDupSets per gene which informs about the number of transcripts sets (equivalence classes by transcript sequence content). + If during the indexing step, user didn’t use –gencode for a Gencode transcriptome file, tximeta will deal with this internally now by stripping all characters after the vertical bar |, in order to match long transcript names in the quant.sf files to the correct transcript names in the GTF.

                   Changes in version 1.5.28                        
  

• Added function splitSE to split one assay of a SummarizedExperiment into multiple assays, each containing features of a given type.

                   Changes in version 1.5.19                        
  

• Added markDuplicateTxps argument to add hasDuplicate and duplicates columns to rowData of SummarizedExperiment. One note is that, for efficiency, this argument and cleanDuplicateTxps will now share a duplicates CharacterList that is stored in the BiocFileCache, with the name dups-.... Therefore, if you have previously used cleanDuplicateTxps, you may need to bfcremove() any dups-... entries. Summarization to gene level will keep track of numDupSets per gene which informs about the number of transcripts sets (equivalence classes by transcript sequence content).

                   Changes in version 1.5.16                        
  

• Added a wrapper function makeDGEList() to simplify making a DGEList for use with edgeR. See vignette for example.

                   Changes in version 1.5.11                        
  

• tximeta can now use customMetaInfo argument to locate a custom metadata information file such as meta_info.json, which should contain a tage, index_seq_hash, with the SHA-256 hash value of the reference transcripts.

                    Changes in version 1.5.8                        
  

• tximeta will now make use of EnsDb created and distributed on AnnotationHub, unless useHub=FALSE. Also, a new function retrieveDb() can be called on a SummarizedExperiment to retrieve the underlying TxDb or EnsDb.

                    Changes in version 1.5.3                        
  

• If during the indexing step, user didn’t use –gencode for a Gencode transcriptome file, tximeta will deal with this internally now by stripping all characters after the vertical bar |, in order to match long transcript names in the quant.sf files to the correct transcript names in the GTF.

tximport

                   Changes in version 1.16.0                        

• Moved alevin arguments into a new ‘list’ argument, alevinArgs. As of this version the possible values for alevinArgs are: filterBarcodes, tierImport, forceSlow (all logical).

• Added alevinArgs argument tierImport, which will import the “tier” information from alevin on the quantification assessment.

• Add an alevinArgs argument filterBarcodes, which will only import cells with barcodes in the whitelist.txt file.

• Fixed bug where the bootstrap matrices from alevin were not aligned by cell with the counts matrix. This affected the variance and the infReps list. The fix will also be propogated to tximport v1.14.1 (Oct 2019 release).

                   Changes in version 1.15.12                       
  

• Moved alevin arguments into a new ‘list’ argument, alevinArgs. As of this version the possible values for alevinArgs are: filterBarcodes, tierImport, forceSlow (all logical).

• Added alevinArgs argument tierImport, which will import the “tier” information from alevin on the quantification assessment.

                   Changes in version 1.15.10                       
  

• Add an alevinArgs argument filterBarcodes, which will only import cells with barcodes in the whitelist.txt file.

                   Changes in version 1.15.9                        
  

• Fixed bug where the bootstrap matrices from alevin were not aligned by cell with the counts matrix. This affected the variance and the infReps list. The fix will also be propogated to tximport v1.14.1 (Oct 2019 release).

UniProt.ws

                   Changes in version 2.27.0                        

BUG FIX

o (2.27.1) Fix bug when selecting column GENEID. The mapping mapped both GENEID and ENTREZ_GENE to P_ENTREZGENE. When returning columsn used match to identify but would only pick up first match which was ENTREZ_GENE entry.

universalmotif

                    Changes in version 1.6.0                        

NEW FEATURES

• log_string_pval(): small utility function to obtain the log of string-formatted p-values (such as those often carried in MEME-formatted motifs which are smaller than R’s double.xmin limit). Likely only a temporary solution.

• view_motifs(…, return.raw) option: instead of returning a plot type object, return the aligned motif matrices.

• view_motifs(…, dedup.names) option: allows plotting of motifs with duplicated names by appending a unique string.

• merge_motifs(…, new.name) option: assign a name to the new merged motif instead of collapsing the names of the merged motifs together.

• round_motif() utility: round down very low letter-position scores to zero.

MINOR CHANGES

• Removed most previously deprecated function arguments.

• Make sure view_motifs(…, use.type = “ICM”) properly sets ylim.

• create_motif(): single motif positions can now be created.

• create_motif(), character input: nsites slot is left empty is input is a single string. It is still filled if the input consists of multiple strings.

• merge_motifs(): ALLR/ALLR_LL/KL/IS methods no longer add pseudocounts to the motifs. Instead, pseudocounts are added to temporary internal copies which are used for comparison and alignment. The original un-modified matrices are then combined.

• read_meme(): now supports DNA-LIKE, RNA-LIKE, and AA-LIKE alphabets, though these will be treated as regular DNA, RNA, and AA alphabets, respectively. Contribution from Spencer Nystrom (https://github.com/bjmt/universalmotif/pull/7).

• Some cleanup to documentation and vignettes.

• General code cleanup.

BUG FIXES

• write_meme() now includes altname slot if filled. Contribution from Spencer Nystrom (https://github.com/bjmt/universalmotif/pull/5).

• write_meme() checks for and removes any spaces/equal signs in motif names/altnames.

• view_motifs(…, use.type = “ICM”): check for zero IC motifs, as these cannot be plotted by ggseqlogo.

variancePartition

                   Changes in version 1.17.10                       

• fix issue returning residuals from limma

• resolve issue where dream gives error: r[cbind(1L:p, 1L:p)] <- 1 : subscript out of bounds - only occured when no fixed effects were used

                   Changes in version 1.17.9                        
  

• Fix issues with compatability with R/4.0.0

                   Changes in version 1.17.8                        
  

• Better error message when response contains missing data

                   Changes in version 1.17.7                        
  

• Better error message when variable in formula does not exist

                   Changes in version 1.17.6                        
  

• comply with new Bioconductor check: R_CHECK_LENGTH_1_LOGIC2

                   Changes in version 1.17.5                        
  

• if contrasts for dream() is data.frame, convert to matrix

                   Changes in version 1.17.4                        
  

• Don’t print warnings for residuals() when only one argument passed.

• fix bug with residuals evaluated with only fixed effects

                   Changes in version 1.17.3                        
  

• Allow sparseMatrix for gene expression. Now saves memory by avoiding conversion to matrix. Processing sparseMatrix will be slower, but memory usage will be low.

• dream(…, computeResiduals=TRUE) now computes residuals and allows use of residuals() function

                   Changes in version 1.17.2                        
  

• fix error in voomWithDreamWeights() when design matrix is null

                   Changes in version 1.17.1                        
  

• topTable(…,sort.by=) now is correct when and F-test is used

• fixed issue in classifyTestsF.MArrayLM2, now is much faster

vasp

            Changes in version 0.99.23 (2020-03-25)                 

• Released to the ‘Devel’ version of Bioconductor (accepted and builded)

             Changes in version 0.99.0 (2020-03-03)                 
  

• Submitted to Bioconductor

ViSEAGO

                     Changes in version 1.1                         

• add gene_symbol field for Custom2GO

• patch for Custom gene_symbols on merge_enrich_terms

• set esummary to 400 terms (instead of 500) by querying on merge_enrich_terms

• add gene frequency hover text on GOterms_heatmap

• add custom heatmap colors on GOterms_heatmap

• showIC print patch on GOterms_heatmap

• GO count update

• Uniprot2GO connection method update

• prevent bioconductor errors when check examples

• annotate upgrade

• merge_enrich_terms upgrade for custom

waddR

             Changes in version 1.1.4 (2020-03-16)                  

• Fixes a build fail due to erronous merge in the previous commit 267f84b

             Changes in version 1.1.3 (2020-03-12)                  
  

• Updates to Documentation

             Changes in version 1.1.2 (2020-03-11)                  
  

• Fixes critical bug: o Removed the usage of the unavailable package ‘eva’, which caused builds to fail

             Changes in version 1.1.1 (2019-10-28)                  
  

• P-value reproducibility feature: o Now using nextRNGstream to generate independent seeds for each gene o Setting the seed (with set.seed()) only in .testWass o Removed use of seeds and the seed argument everywhere in WassersteinTest.R

weitrix

                   Changes in version 0.99.2                        

• Automatic package builder wants package to depend on R version 4.0.

                   Changes in version 0.99.1                        
  

• weitrix now uses the BiocParallel default parallel processing, rather than the DelayedArray default. (DelayedArray does not use parallel processing by default as of version 0.14.0.)

                   Changes in version 0.99.0                        
  

• Bioconductor submission.

                    Changes in version 0.1.0                        
  

• Initial version.

xcms

                    Changes in version 3.9.4                        

• Fix issue in centWave which skips peak detection depending on minimum peakwidth (issue #445): add parameter extendLengthMSW in CentWaveParam. Thanks to William Kumler for contributing the fix.

• Tentatively reduce memory requirements in fillChromPeaks.

• Fix issue #467 for fillPeaks() of an xcmsSet converted from an XCMSnSet

                    Changes in version 3.9.3                        
  

• Move multtest from Imports to Suggests to avoid duplicated method definition for plot (issue #459).

• Add support for peak filling from MS level > 1 to fillChromPeaks.

• featureValues gains parameter msLevel to extract feature values for features of all, or from a specific MS level.

• refineChromPeaks supports different MS levels.

• Added support to perform correspondence analysis on MS level > 1 and add the respective results to already present feature definitions.

• hasChromPeaks and hasFeatures gain parameter msLevel to check for presence of chromatographic peaks or features from a specific MS level.

                    Changes in version 3.9.2                        
  

• Fix featureChromatograms and chromatograms on a XCMSnExp object with features: features can be duplicated across rows (EICs).

• findChromPeaks: add parameter add to allow several rounds of peak detections on the same object.

• Small performance enhancement in fillChromPeaks.

• Better support for MS > 1 data in fillChromPeaks: skip MS level 2 spectra for filling in.

• Add refineChromPeaks for XChromatogram and XChromatograms objects.

• Add groupOverlaps function to group arbitrary ranges.

• Add quantify,XCMSnExp object to quantify an XCMSnExp into a SummarizedExperiment.

• Fine-tune MergeNeighboringPeaks peak refinement method: the average of the 3 data points between candidate peaks is used to evaluate whether the peaks should be merged making the approach more robust against outliers. In addition, an ion chromatogram for candidate peaks is extracted with an m/z range expanded depending on the expandMz and ppm setting ensuring that low intensity data points between candidate peaks are not missed out (because their m/z might be slightly shifted on ToF instruments). The mzmin and mzmax of the merged peak represents also the minimum and maximum m/z of all data points in that extracted ion chromatogram.

                    Changes in version 3.9.1                        
  

• Fix problem of not shown/plotted peak positions in plotChromPeakSpectra for experiments in which peaks were not detected in the first sample(s).

• Add method from_to to missing value imputation method imputeRowMinRand.

• Show warning in findChromPeaks if empty spectra are detected.

• Add refineChromPeaks method and CleanPeaksParam class to allow removal of chromatographic peaks exceeding a user-definable maximal peak width.

• Add MergeNeighboringPeaksParam for refineChromPeaks to allow merging of chromatographic peaks close in m/z and retention time with a signal between them higher than a certain threshold (issue #414).

• Fix misspelled parameter mzd in LC-MS/MS vignette.

YAPSA

                   Changes in version 1.13.3                        

This is a stable version after several important changes

• 95% Confidence intervals for exposures to mutational signatures can be computed

• Analysis of the PCAWG mutational signatures is supported, both for PCAWG SNV and PCAWG Indel signatures

The vignettes have been substantially changed

• new vignettes have been written for the new features confidence intervals and Indel signatures

• new vignettes were added for features already present in the package before, especially the optimal signature-specific cutoffs

• the topic of stratifiec analyses of mutational signatures was taken out of the main vignette and now is described in a vignette on its own.

NEWS from new and existing Data Experiment Packages

curatedAdipoArray

             Changes in version 0.99.0 (2019-10-10)                 

• Submitted to Bioconductor

depmap

Changes in Version 1.1.2

• 20Q1 data added

Changes in Version 1.1.1

• 19Q4 data added
• Updated loading functions (accessor functions)
• 19Q4 versions of rnai, RPPA and drug_sensitivity were not released for this quarter, and therefore the 19Q3 releases for these datasets are the most current versions.

derfinderData

                    Changes in version 2.5.3                        

SIGNIFICANT USER-VISIBLE CHANGES

• Now using BiocStyle for the vignette.

                    Changes in version 2.5.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://leekgroup.github.io/derfinderData/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

dorothea

             Changes in version 0.99.9 (2020-04-22)                 

• Integration of Travis CI

• Integrated unit test coverage with codecov

• Build github page via pkgdown

             Changes in version 0.99.1 (2020-04-06)                 
  

• If the input to the viper wrapper is a Bioconductor class, this Bioconductor class is retured with added TF activities at appropiate slots

• Expanded the viper wrapper to the Bioconductor class SingleCellExperiment

             Changes in version 0.99.0 (2020-04-03)                 
  

• Initial submission to Bioconductor

dsQTL

                    Changes in version 2.17                         

USER VISIBLE CHANGES

• ch2locs (retrievable via dsQTL::getSNPlocs) has been changed at about 1850 locations where rs numbers had been associated with hg19 addresses; the dsQTL regions are hg18 as are all the chr2… SNP addresses. Previously the discoverable rs numbers used in the Chicago distribution from http://eqtl.uchicago.edu/dsQTL_data/GENOTYPES/ had be mapped via SNPlocs…20111119, but now they come directly from the Chicago text file.

FlowSorted.Blood.EPIC

             Changes in version 1.5.2 (2019-11-05)                  

• Made the following significant changes o Added the projectCellType_CP function for projecting the cell counts on beta values

HDCytoData

                    Changes in version 1.6.3                        

• Add vignette “Examples and use cases”

• Add vignette “Contribution guidelines”

• Update documentation

HighlyReplicatedRNASeq

                   Changes in version 0.99.0                        

• Initial release of the package

pRolocdata

                   Changes in version 1.25.3                        

• update email

                   Changes in version 1.25.2                        
  

• add data from Shin et al. (2020)

• add data from Baryluk et al. (2020)

                   Changes in version 1.25.1                        
  

• add dynamic Itzhak data

PtH2O2lipids

                 Changes in version 2016-04-21                      

• Initial release for Bioconductor

RegParallel

                    Changes in version 1.6.0                        

• vignette updates

• removed glm.nb

RNAmodR.Data

              Changes in version 1.1 (2020-02-13)                   

• Fixed snoRNAdb information regarding positions of RNU12 modifications and RNU2 modification type at position 11 and 61

scRNAseq

                    Changes in version 2.2.0                        

• Removed deprecated inbuilt datasets.

scTHI.data

             Changes in version 0.99.6 (2020-03-02)                 

• Submitted to Bioconductor

signatureSearchData

             Changes in version 1.1.0 (2019-10-23)                  

• Initial version

WGSmapp

                   Changes in version 0.99                        

• Add mm10 blacklist regions
• Use lazy-loading of data
• Update R version Dependency to 3.6
• Fix NAs in seqlengths(mapp_hg38)
• Incorporate hg38gaps.txt
• Add seg region file for hg38
• Bump version number to trigger a new build
• Remove WGSmapp.Rproj and add GenomicRanges dependency
• WGSmapp getting ready for submission to Bioc

NEWS from new and existing Workflows

fluentGenomics

                   Changes in version 0.99.0                        

• Added a NEWS.md file to track changes to the package.

recountWorkflow

                   Changes in version 1.11.2                        

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://LieberInstitute.github.io/recountWorkflow/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown. - Added a NEWS.md file to track changes to the package.

BUG FIXES

• Fix the spelling of RIN to rin now that all SRA columns are in lower case. - Fix the DESCRIPTION file (had a missing comma).

                   Changes in version 1.11.1                        
  

NEW FEATURES

• Piggyback on GenomicState now that this package produces all the pieces needed for making the ER plots. - Potentially everything works on Windows now that rtracklayer::import.bw() seems to work there. But I haven’t tested it.

BUG FIXES

• Update SRARunTable.txt reading code since they changed the format on delivered by SRA. Adjust variables accordingly.

Deprecated and Defunct Packages

Eighteen software packages were removed from this release (after being deprecated in Bioc 3.10): birte, brainImageR, charm, CNPBayes, condcomp, dSimer, exomePeak, flipflop, GenomeGraphs, HTSanalyzeR, mlm4omics, Pbase, plateCore, Rchemcpp, rHVDM, RnaSeqSampleSize, SEPA, SNPchip

Fifty Six software are deprecated in this release and will be removed in Bioc 3.12: affypdnn, AnalysisPageServer, anamiR, BayesPeak, bgafun, biosvd, birta, CALIB, CAMTHC, cellGrowth, chroGPS, cobindR, CTDquerier, CVE, DChIPRep, DEDS, DupChecker, FEM, gCMAP, gCMAPWeb, geecc, Genominator, IdMappingAnalysis, IdMappingRetrieval, IPPD, kimod, LMGene, lol, LVSmiRNA, M3D, manta, MaxContrastProjection, MCRestimate, MergeMaid, mitoODE, MoPS, motifRG, MTseeker, nem, PAPi, pcaGoPromoter, pint, plw, PowerExplorer, proteoQC, QUALIFIER, readat, RefNet, RIPSeeker, SANTA, scfind, splicegear, sRAP, triform, Vega, waveTiling

DESeq has been deprecated in favor of DESeq2. Due to its high number of reverse dependencies it will remain deprecated in 3.12 to be removed in 3.13.

Three experimental data packages were removed in this release (after being deprecated in BioC 3.10): allenpvc, charmData, facopy.annot

Two experimental data packages are deprecated in this release and will be removed in Bioc 3.12: MTseekerData, RIPSeekerData

Two annotation packages were removed this release: MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38

Nine annotation packages are deprecated in this release and will be removed in Bioc 3.12: hom.At.inp.db, hom.Ce.inp.db, hom.Dm.inp.db, hom.Dr.inp.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db, KEGG.db.

One workflow package is removed in this release (after being deprecated in BioC 3.10): BgeeCall (This package has moved to Software)

No workflow packages were deprecated in this release.