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• Bioconductor 3.20 Released

October 30, 2024

Bioconductor:

We are pleased to announce Bioconductor 3.20, consisting of 2289 software packages, 431 experiment data packages, 928 annotation packages, 30 workflows and 5 books.

There are 54 new software packages, 5 new data experiment packages, 4 new annotation packages, no new workflows, no new books, and many updates and improvements to existing packages.

Bioconductor 3.20 is compatible with R 4.4, and is supported on Linux, 64-bit Windows, Intel 64-bit macOS 11 (Big Sur) or higher, macOS arm64 and Linux arm64. This release will also include updated Bioconductor Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

• Getting Started with Bioconductor 3.20
• New Software Packages
• New Data Experiment Packages
• New Annotation Packages
• New Workflow
• New Books
• NEWS from existing software packages
• NEWS from existing data experiment packages
• NEWS from existing workflows
• Deprecated and Defunct Packages

Getting Started with Bioconductor 3.20

To update to or install Bioconductor 3.20

1. Install R 4.4. Bioconductor 3.20 has been designed expressly for this version of R.

2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 54 new software packages in this release of Bioconductor.

• ADAPT ADAPT carries out differential abundance analysis for microbiome metagenomics data in phyloseq format. It has two innovations. One is to treat zero counts as left censored and use Tobit models for log count ratios. The other is an innovative way to find non-differentially abundant taxa as reference, then use the reference taxa to find the differentially abundant ones.

• AnVILAz The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVILAz package supports end-users and developers using the AnVIL platform in the Azure cloud. The package provides a programmatic interface to AnVIL resources, including workspaces, notebooks, tables, and workflows. The package also provides utilities for managing resources, including copying files to and from Azure Blob Storage, and creating shared access signatures (SAS) for secure access to Azure resources.

• AnVILBase Provides generic functions for interacting with the AnVIL ecosystem. Packages that use either GCP or Azure in AnVIL are built on top of AnVILBase. Extension packages will provide methods for interacting with other cloud providers.

• AnVILGCP The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to work with the AnVIL package. User-level interaction with this package should be minimal.

• assorthead Vendors an assortment of useful header-only C++ libraries. Bioconductor packages can use these libraries in their own C++ code by LinkingTo this package without introducing any additional dependencies. The use of a central repository avoids duplicate vendoring of libraries across multiple R packages, and enables better coordination of version updates across cohorts of interdependent C++ libraries.

• BioGA Genetic algorithm are a class of optimization algorithms inspired by the process of natural selection and genetics. This package allows users to analyze and optimize high throughput genomic data using genetic algorithms. The functions provided are implemented in C++ for improved speed and efficiency, with an easy-to-use interface for use within R.

• broadSeq This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.

• CatsCradle This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. ‘CatsCradle’ allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.

• CleanUpRNAseq RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.

• DeepTarget This package predicts a drug’s primary target(s) or secondary target(s) by integrating large-scale genetic and drug screens from the Cancer Dependency Map project run by the Broad Institute. It further investigates whether the drug specifically targets the wild-type or mutated target forms. To show how to use this package in practice, we provided sample data along with step-by-step example.

• DFplyr Provides dplyr verbs (mutate, select, filter, etc…) supporting S4Vectors::DataFrame objects. Importantly, this is achieved without conversion to an intermediate tibble. Adds grouping infrastructure to DataFrame which is respected by the transformation verbs.

• dominoSignal dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from CellPhoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.

• DuplexDiscovereR DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts input in the form of chimerically or split-aligned reads. It includes procedures for alignment classification, filtering, and efficient clustering of individual chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts RNA duplex formation and their hybridization energies. Additional metrics, such as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated to rank final set of RNA duplexes. Data from multiple experiments or replicates can be processed separately and further compared to check the reproducibility of the experimental method.

• EnrichDO To implement disease ontology (DO) enrichment analysis, this package is designed and presents a double weighted model based on the latest annotations of the human genome with DO terms, by integrating the DO graph topology on a global scale. This package exhibits high accuracy that it can identify more specific DO terms, which alleviates the over enriched problem. The package includes various statistical models and visualization schemes for discovering the associations between genes and diseases from biological big data.

• EpipwR A quasi-simulation based approach to performing power analysis for EWAS (Epigenome-wide association studies) with continuous or binary outcomes. ‘EpipwR’ relies on empirical EWAS datasets to determine power at specific sample sizes while keeping computational cost low. EpipwR can be run with a variety of standard statistical tests, controlling for either a false discovery rate or a family-wise type I error rate.

• funOmics The ‘funOmics’ package ggregates or summarizes omics data into higher level functional representations such as GO terms gene sets or KEGG metabolic pathways. The aggregated data matrix represents functional activity scores that facilitate the analysis of functional molecular sets while allowing to reduce dimensionality and provide easier and faster biological interpretations. Coordinated functional activity scores can be as informative as single molecules!

• geomeTriD geomeTriD (Three Dimensional Geometry Package) create interactive 3D plots using the GL library with the ‘three.js’ visualization library (https://threejs.org) or the rgl library. In addition to creating interactive 3D plots, the application also generates simplified models in 2D. These 2D models provide a more straightforward visual representation, making it easier to analyze and interpret the data quickly. This functionality ensures that users have access to both detailed three-dimensional visualizations and more accessible two-dimensional views, catering to various analytical needs.

• ggseqalign Simple visualizations of alignments of DNA or AA sequences as well as arbitrary strings. Compatible with Biostrings and ggplot2. The plots are fully customizable using ggplot2 modifiers such as theme().

• HoloFoodR Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.

• HuBMAPR ‘HuBMAP’ provides an open, global bio-molecular atlas of the human body at the cellular level. The datasets(), samples(), donors(), publications(), and collections() functions retrieves the information for each of these entity types. *_details() are available for individual entries of each entity type. *_derived() are available for retrieving derived datasets or samples for individual entries of each entity type. Data files can be accessed using files_globus_url().

• immApex A set of tools to build tensorflow/keras-based models in R from amino acid and nucleotide sequences focusing on adaptive immune receptors. The package includes pre-processing of sequences, unifying gene nomenclature usage, encoding sequences, and combining models. This package will serve as the basis of future immune receptor sequence functions/packages/models compatible with the scRepertoire ecosystem.

• immunogenViewer Plots protein properties and visualizes position of peptide immunogens within protein sequence. Allows evaluation of immunogens based on structural and functional annotations to infer suitability for antibody-based methods aiming to detect native proteins.

• iSEEtree iSEEtree is an extension of iSEE for the TreeSummarizedExperiment. It leverages the functionality from the miaViz package for microbiome data visualisation to create panels that are specific for TreeSummarizedExperiment objects. Not surprisingly, it also depends on the generic panels from iSEE.

• kmcut The purpose of the package is to identify prognostic biomarkers and an optimal numeric cutoff for each biomarker that can be used to stratify a group of test subjects (samples) into two sub-groups with significantly different survival (better vs. worse). The package was developed for the analysis of gene expression data, such as RNA-seq. However, it can be used with any quantitative variable that has a sufficiently large proportion of unique values.

• koinar A client to simplify fetching predictions from the Koina web service. Koina is a model repository enabling the remote execution of models. Predictions are generated as a response to HTTP/S requests, the standard protocol used for nearly all web traffic.

• MetMashR A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the struct package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.

• MOSClip Topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.

• MPAC Multi-omic Pathway Analysis of Cancer (MPAC), integrates multi-omic data for understanding cancer mechanisms. It predicts novel patient groups with distinct pathway profiles as well as identifying key pathway proteins with potential clinical associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA states (i.e., repressed, normal, or activated), which serve as the input for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes DNA and RNA states to create a background distribution to filter IPLs as a way to remove events observed by chance. It provides multiple methods for downstream analysis and visualization.

• MsBackendMetaboLights MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.

• OmicsMLRepoR This package provides functions to browse the harmonized metadata for large omics databases. This package also supports data navigation if the metadata incorporates ontology.

• omXplore This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.

• PepSetTest Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights.

• Pirat Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.

• plyxp The package provides rlang data masks for the SummarizedExperiment class. The enables the evaluation of unquoted expression in different contexts of the SummarizedExperiment object with optional access to other contexts. The goal for plyxp is for evaluation to feel like a data.frame object without ever needing to unwind to a rectangular data.frame.

• PolySTest The complexity of high-throughput quantitative omics experiments often leads to low replicates numbers and many missing values. We implemented a new test to simultaneously consider missing values and quantitative changes, which we combined with well-performing statistical tests for high confidence detection of differentially regulated features. The package contains functions to run the test and to visualize the results.

• PRONE High-throughput omics data are often affected by systematic biases introduced throughout all the steps of a clinical study, from sample collection to quantification. Normalization methods aim to adjust for these biases to make the actual biological signal more prominent. However, selecting an appropriate normalization method is challenging due to the wide range of available approaches. Therefore, a comparative evaluation of unnormalized and normalized data is essential in identifying an appropriate normalization strategy for a specific data set. This R package provides different functions for preprocessing, normalizing, and evaluating different normalization approaches. Furthermore, normalization methods can be evaluated on downstream steps, such as differential expression analysis and statistical enrichment analysis. Spike-in data sets with known ground truth and real-world data sets of biological experiments acquired by either tandem mass tag (TMT) or label-free quantification (LFQ) can be analyzed.

• rhinotypeR “rhinotypeR” is designed to automate the comparison of sequence data against prototype strains, streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, this package makes genotype assignment accessible to researchers and public health professionals. This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. Additionally, “rhinotypeR” supports comprehensive visualization and analysis of single nucleotide polymorphisms (SNPs) and amino acid substitutions, facilitating in-depth genetic and evolutionary studies.

• scDiagnostics The scDiagnostics package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles. The implemented functionality allows to assess the reliability of cell type annotations, investigate gene expression patterns, and explore relationships between different cell types in query and reference datasets allowing users to detect potential misalignments between reference and query datasets. The package also provides visualization capabilities for diagnostics purposes.

• scDotPlot Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.

• scoup An elaborate molecular evolutionary framework that facilitates straightforward simulation of codon genetic sequences subjected to different degrees and/or patterns of Darwinian selection. The model was built upon the fitness landscape paradigm of Sewall Wright, as popularised by the mutation-selection model of Halpern and Bruno. This enabled realistic evolutionary process of living organisms to be reproduced seamlessly. For example, an Ornstein-Uhlenbeck fitness update algorithm is incorporated herein. Consequently, otherwise complex biological processes, such as the effect of the interplay between genetic drift and mutation on the inference of diversifying selection, may now be investigated with minimal effort. Frequency-dependent and deterministic fitness landscape update techniques are also available.

• scrapper Implements R bindings to C++ code for analyzing single-cell (expression) data, mostly from various libscran libraries. Each function performs an individual step in the single-cell analysis workflow, ranging from quality control to clustering and marker detection. It is mostly intended for other Bioconductor package developers to build more user-friendly end-to-end workflows.

• seahtrue Seahtrue organizes oxygen consumption and extracellular acidification analysis data from experiments performed on an XF analyzer into structured nested tibbles.This allows for detailed processing of raw data and advanced data visualization and statistics. Seahtrue introduces an open and reproducible way to analyze these XF experiments. It uses file paths to .xlsx files. These .xlsx files are supplied by the userand are generated by the user in the Wave software from Agilent from the assay result files (.asyr). The .xlsx file contains different sheets of important data for the experiment; 1. Assay Information - Details about how the experiment was set up. 2. Rate Data - Information about the OCR and ECAR rates. 3. Raw Data - The original raw data collected during the experiment. 4. Calibration Data - Data related to calibrating the instrument. Seahtrue focuses on getting the specific data needed for analysis. Once this data is extracted, it is prepared for calculations through preprocessing. To make sure everything is accurate, both the initial data and the preprocessed data go through thorough checks.

• SpaNorm This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.

• spatialSimGP This packages simulates spatial transcriptomics data with the mean- variance relationship using a Gaussian Process model per gene.

• SpectraQL The Mass Spec Query Language (MassQL) is a domain-specific language enabling to express a query and retrieve mass spectrometry (MS) data in a more natural and understandable way for MS users. It is inspired by SQL and is by design programming language agnostic. The SpectraQL package adds support for the MassQL query language to R, in particular to MS data represented by Spectra objects. Users can thus apply MassQL expressions to analyze and retrieve specific data from Spectra objects.

• squallms squallms is a Bioconductor R package that implements a “semi-labeled” approach to untargeted mass spectrometry data. It pulls in raw data from mass-spec files to calculate several metrics that are then used to label MS features in bulk as high or low quality. These metrics of peak quality are then passed to a simple logistic model that produces a fully-labeled dataset suitable for downstream analysis.

• StabMap StabMap performs single cell mosaic data integration by first building a mosaic data topology, and for each reference dataset, traverses the topology to project and predict data onto a common embedding. Mosaic data should be provided in a list format, with all relevant features included in the data matrices within each list object. The output of stabMap is a joint low-dimensional embedding taking into account all available relevant features. Expression imputation can also be performed using the StabMap embedding and any of the original data matrices for given reference and query cell lists.

• survClust survClust is an outcome weighted integrative clustering algorithm used to classify multi-omic samples on their available time to event information. The resulting clusters are cross-validated to avoid over overfitting and output classification of samples that are molecularly distinct and clinically meaningful. It takes in binary (mutation) as well as continuous data (other omic types).

• tidyFlowCore tidyFlowCore bridges the gap between flow cytometry analysis using the flowCore Bioconductor package and the tidy data principles advocated by the tidyverse. It provides a suite of dplyr-, ggplot2-, and tidyr-like verbs specifically designed for working with flowFrame and flowSet objects as if they were tibbles; however, your data remain flowCore data structures under this layer of abstraction. tidyFlowCore enables intuitive and streamlined analysis workflows that can leverage both the Bioconductor and tidyverse ecosystems for cytometry data.

• tidysbml Starting from one SBML file, it extracts information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i.e. either compartment, species, reaction or speciesReference) and one set of columns for the attributes, one column for the content of the ‘notes’ subelement and one set of columns for the content of the ‘annotation’ subelement.

• tidytof This package implements an interactive, scientific analysis pipeline for high-dimensional cytometry data built using tidy data principles. It is specifically designed to play well with both the tidyverse and Bioconductor software ecosystems, with functionality for reading/writing data files, data cleaning, preprocessing, clustering, visualization, modeling, and other quality-of-life functions. tidytof implements a “grammar” of high-dimensional cytometry data analysis.

• TMSig The TMSig package contains tools to prepare, analyze, and visualize named lists of sets, with an emphasis on molecular signatures (such as gene or kinase sets). It includes fast, memory efficient functions to construct sparse incidence and similarity matrices and filter, cluster, invert, and decompose sets. Additionally, bubble heatmaps can be created to visualize the results of any differential or molecular signatures analysis.

• xenLite Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.

• zitools zitools allows for zero inflated count data analysis by either using down-weighting of excess zeros or by replacing an appropriate proportion of excess zeros with NA. Through overloading frequently used statistical functions (such as mean, median, standard deviation), plotting functions (such as boxplots or heatmap) or differential abundance tests, it allows a wide range of downstream analyses for zero-inflated data in a less biased manner. This becomes applicable in the context of microbiome analyses, where the data is often overdispersed and zero-inflated, therefore making data analysis extremly challenging.

New Data Experiment Packages

There are 5 new data experiment packages in this release of Bioconductor.

• bugphyzz bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods.

• eoPredData Provides access to eoPred pretrained model hosted on ExperimentHub. Model was trained on placental DNA methylation preeclampsia samples using mixOmics splsda. There are two resources: 1. the model object, and 2. a testing data set used to demonstrate the function.

• EpipwR.data This package provides reference data for EpipwR. EpipwR is a fast and efficient power analysis for continuous and binary phenotypes of epigenomic-wide association studies. This package is only meant to be used in conjunction with EpipwR.

• LegATo LegATo is a suite of open-source software tools for longitudinal microbiome analysis. It is extendable to several different study forms with optimal ease-of-use for researchers. Microbiome time-series data presents distinct challenges including complex covariate dependencies and variety of longitudinal study designs. This toolkit will allow researchers to determine which microbial taxa are affected over time by perturbations such as onset of disease or lifestyle choices, and to predict the effects of these perturbations over time, including changes in composition or stability of commensal bacteria.

• ProteinGymR The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. Deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. AlphaMissense pathogenicity scores for ~1.6 M substitutions in the ProteinGym DMS data, and 3. five performance metrics for 62 variant prediction models in a zero-shot setting.

New Annotation Packages

There are 4 new annotation packages.

• HDO.db A set of annotation maps describing the entire Human Disease Ontology assembled using data from DO. Its annotation data comes from https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology

• IlluminaHumanMethylationMSAanno.ilm10a1.hg38 An annotation package for Illumina’s MSA methylation arrays.

• IlluminaHumanMethylationMSAmanifest A manifest package for use with Illumina’s MSA methylation arrays, compatible with minfi.

• TENET.AnnotationHub AnnotationHub package containing datasets for use in the TENET package. Includes GenomicRanges objects representing putative enhancer, promoter, and open chromatin regions. All included datasets are aligned to the hg38 human genome.

New Workflow Packages

There are no new workflow packages in this release of Bioconductor.

New Online Books

There are no new books in this release of Bioconductor.

NEWS from existing Software Packages

alabaster.base

                    Changes in version 1.6.0                        

• Distinguish between scalars and length-1 vectors when saving/loading lists. This effectively unboxes all length-1 vectors in a list, by default; this is probably the more reasonable expectation for other languages that have a concept of scalars. Users can override this by calling I() on elements that they want to keep as length-1 vectors, in the same manner as jsonlite.

• Streamlined the definition of the Rfc3339 class so that it behaves better with I().

• Normalize paths to resolve ~ prior to calling C++ code.

• Open HDF5 files in read-only mode to avoid permission-related problems for readObject()-dispatched functions.

• Store numbers at maximum precision when saving lists in the JSON format via saveObject().

• Added registerValidateObjectSatisfiesInterface() and registerValidateObjectDerivedFrom(), to allow developers to declare that custom subclasses satisfy an interface or have an inheritance relationship, respectively.

• Updated validateDirectory() so that it works with a directory of objects saved via saveObject(). Objects saved under the old regime (i.e., stageObject()) are auto-detected but can also be explicitly validated by setting legacy=FALSE.

• Added a data.frame method for saveObject(), to avoid fallback to the list method.

alabaster.mae

                    Changes in version 1.6.0                        

• Respect application-level overrides when saving child components of a MultiAssayExperiment.

alabaster.matrix

                    Changes in version 1.6.0                        

• Support the SVT_SparseMatrix version 1 class definition in saveObject(). However, note that this was not implemented for the soft-deprecated writeSparseMatrix(), which now errors if such objects are passed in.

• Added a extract_sparse_array() method for the WrapperArraySeed class, for some future-proofing when the seeds eventually make the switch.

• Bugfix for integer overflow when saving large sparse matrices in saveObject().

• Open all HDF5 files in read-only mode for readObject() dispatch functions, to avoid permission-related issues.

• Added altReloadDelayedObject(), altStoreDelayedObject(), and their associated getters/setters, to allow applications to override the delayed operation saving/reading process.

• Added registerReloadDelayedObjectFunction() to allow extension developers to register reader functions for new classes.

• Added a ReloadedArray.reuse.files=”relsymlink” option in the saveObject() method for ReloadedArrays. This creates relative symbolic links to the original array files, which is more robust to their movement provided the linked files are moved in the same manner.

• Enable deduplication of identical seeds across multiple calls to storeDelayedObject() within a single “session”. This avoids making multiple copies of the same seed for different DelayedArray instances with the same seeds, e.g., in a SummarizedExperiment.

• Added an external.save.args= option to storeDelayedObject() to avoid conflicts in the method arguments of saveObject().

alabaster.ranges

                    Changes in version 1.6.0                        

• Open HDF5 files in read-only mode to avoid permission-related problems for readObject()-dispatched functions.

• Use altSaveObject() when saving child components inside saveObject() methods.

alabaster.se

                    Changes in version 1.6.0                        

• Preserve row names when setting the rowRanges in readRangedSummarizedExperiment.

alabaster.spatial

                    Changes in version 1.6.0                        

• Dispatch to saveObject() for any of the SpatialExperiment’s images that implement a dedicated method for it.

AlphaMissenseR

                    Changes in version 1.2.0                        

• (v. 1.1.9) Manage duckdb connections more completely; all registered connections are disconnected (invalidated) whenever a new table is created.
• (v. 1.1.7) Add ‘Benchmarking with ProteinGym’ vignette to benchmark AlphaMissense predictions. https://github.com/mtmorgan/AlphaMissenseR/pull/8. Thank you @tram-nguyen-n
• (v. 1.1.6) Add gosling_plot() for visualizing variants as bar or lollipop plots. Merges https://github.com/mtmorgan/AlphaMissenseR/pull/6 Thanks @lee-t.
• (v. 1.1.4) Add clinvar_data() and clinvar_plot() for visualizing ClinVar data. Merges https://github.com/mtmorgan/AlphaMissenseR/pull/4 Thanks @tram-nguyen-n
• (v. 1.1.2) af_predictions() returns a tibble with 21 columns, instead of 20. Merges https://github.com/mtmorgan/AlphaMissenseR/pull/3.

AlpsNMR

             Changes in version 4.7.2 (2024-08-10)                  

• Disable nested parallellization in nmr_detect_peaks_tune_snr().

             Changes in version 4.7.1 (2024-06-02)                  
  

• Added nmr_autophase() for automated phase correction using the NMRphasing package (#68).
• Added to_ASICS function to export dataset for ASICS quantification (#68).

AnnotationForge

                   Changes in version 1.48.0                        

BUG FIXES AND MINOR IMPROVEMENTS

• Updated viableIDs.rda file in extdata directory (@lshep)

• Added rmarkdown to Suggests in DESCRIPTION file

AnnotationHub

                   Changes in version 3.13.0                        

BUG CORRECTION

• (3.13.1) merged @votti PR for not checking connection if localhub is selected

NEW FEATURES

• (3.13.2) Add auto clean of cache if corrupt index file

• (3.13.3) Add auto redownload once if resource is not loading in R, if localHub is not selected and internet available.

AnVIL

                   Changes in version 1.18.0                        

USER VISIBLE CHANGES

• (v 1.17.18) Added has_avworkspace function to check for the existence of an AnVIL workspace environment.

• (v 1.17.10) Internal functions now use AnVILGCP for gcloud utilities.

• (v 1.17.8) Functions that use gcloud utilities are deprecated and will be moved to AnVILGCP. See help(package = “AnVIL”) for a complete list. Documentation pages have a *-deprecated suffix.

• (v 1.17.3) Added Terra Data Repository (TDR) service as TDR(). See service at https://data.terra.bio.

• (v 1.17.1) Gen3 services, avworkflow*_configuration() functions, install(), repository(), and repositories() have been removed.

• (v 1.17.1) Defunct repository_stats function in favor of BiocPkgTools::repositoryStats (@LiNk-NY)

BUG FIXES AND MINOR IMPROVEMENTS

• (v 1.17.20) Use lifeCycle from BiocBaseUtils to mark functions as deprecated or defunct.

• (v 1.17.19) Increase robustness of gcloud_exists by testing gcloud with the version command.

• (v 1.17.18) Remove mentions of AnVIL::install from the vignette.

• (v 1.17.13) Update to changes in rapiclient and use native pipe operator.

• (v 1.17.7) Do not evaluate vignette chunks if gcloud_exists() is FALSE

• (v 1.17.6) Update Dockstore API file, version, and URL

• (v 1.17.2) Use application/json as default Content-Type.

ATACseqQC

                   Changes in version 1.29.1                        

• Fix the space inserted at the beginning after formatC for exportBamFile.

basilisk

                   Changes in version 1.18.0                        

• Switch to the latest Miniforge installer (24.3.0-0) by default. This is preconfigured to use the conda-forge channel and avoids issues with the non-FOSS licensing of the Anaconda repositories. Users can switch back to the old Miniconda installer by setting the BASILISK_USE_MINIFORGE=0 environment variable, but this will likely be deprecated in the next release.

• Channel specifications in the user’s .condarc are now ignored. Only the channels by the developer in setupBasiliskEnv() (e.g., via BasiliskEnvironment) will be respected, to improve the consistency of the constructed environments across devices.

basilisk.utils

                   Changes in version 1.18.0                        

• Switch to the latest Miniforge installer (24.3.0-0) by default. This is preconfigured to use the conda-forge channel and avoids issues with the non-FOSS licensing of the Anaconda repositories. Users can switch back to the old Miniconda installer by setting the BASILISK_USE_MINIFORGE=0 environment variable, but this will likely be deprecated in the next release.

• Update the reticulate version in the fallback environment to 1.38.

BatchQC

                    Changes in version 2.1.6                        

Bug Fixes

• Corrected code for proper division of less than or 20+ samples

#Version 2.1.5

bug Fixes

• Coerce variable of interest to a factor

                    Changes in version 2.1.4                        
  

Major Changes

• Added negative binomial check for 20+ samples to DESeq2

                    Changes in version 2.1.3                        
  

Major Changes

• Added negative binomial check for less than 20 samples to DESeq2

                    Changes in version 2.1.2                        
  

Major Changes

• Added Variation Ratio Statistic to the explained variation tab

Minor Changes

• Removed extra “Samples” column from example data

• Uploaded bladder example data batch variable as a factor

                    Changes in version 2.1.1                        
  

Bug Fixes

• Updated imports to include shinyjs
• Updated imports to remove dendextend which is no longer utilized
• Corrected typos in Intro vignette

BayesSpace

                   Changes in version 1.15.3                        

Minor improvements and fixes

• Minor improvement of code style

                   Changes in version 1.15.2                        
  

Minor improvements and fixes

• Minor bugfixes related to R install, build, check

• Documentation improvements

                   Changes in version 1.15.1                        
  

Major updates

• Accelerate resolution enhancement with multithreaded spatialEnhance
• Improve mixing of MCMC for spatialEnhance with adaptive MCMC
• Support VisiumHD

Minor improvements and fixes

• Support SpaceRanger v2.0+
• Find the optimal number of cores with coreTune before enhancing resolution
• Adjust the proportion of samples to be removed during burnin using adjustClusterLabels
• Faster neighbor finding for subspots

• Customize resolution enhancement for VisiumHD data

                   Changes in version 1.15.0                        
  

New Bioconductor devel (3.20)

• Version numbering change with Bioconductor version bump

beachmat

                   Changes in version 2.22.0                        

• Moved all C++ libraries to the assorthead package. This uses the latest versions of the tatami framework.

• Automatically attempt to use beachmat.hdf5 (if installed) when encountering the various HDF5Array classes.

• Minor optimization when dealing with some known no-op matrices, e.g., WrapperArraySeed objects from alabaster.matrix.

• Map delayed type coercions from type<- to their corresponding native representations (or no-ops).

• Bugfix for initializeCpp() to work properly with dense Matrix instances.

• Soft-deprecated whichNonZero() in favor of SparseArray’s new nzwhich() and nzvals() functions.

• Exported tatami.* utilities for manipulating already-initialized pointers from initializeCpp(). This includes all of the delayed operation wrappers, some previously internal functions for extracting matrix data, a new function for realizing the matrix into a standard R representation, and a new function for matrix multiplication.

beachmat.hdf5

                    Changes in version 1.4.0                        

• Migrated C++ libraries to the assorthead package. Also switch to the latest version fo the tatami_hdf5 library.

• Use the DelayedArray block size as the cache size limit during construction of tatami_hdf5::DenseMatrix, etc.

BgeeDB

                    Changes in version 2.32                         

• Allows to download data from Bgee 15.2 with more bulk RNA-Seq and single-cell RNA-Seq

• Possibility to download h5ad single-cell data with the function getCellProcessedData

• Possibility to download integrated Bgee gene expression calls similar to Bgee gene page results with the function getIntegratedCalls

• topAnat has been optimized to run faster

• The getData function has been deprecated and replaced by the function getSampleProcessedData

BiocGenerics

                   Changes in version 0.52.0                        

NEW FEATURES

• Define the OutOfMemoryObject class (VIRTUAL class with no slots).

• Add S4 generic containsOutOfMemoryData() and implement various methods. See ‘?containsOutOfMemoryData’ for the details.

• Add S4 generic saveRDS() and a default method that is just a thin wrapper around base::saveRDS() that issues a warning if the object to serialize contains out-of-memory data.

BiocNeighbors

                   Changes in version 1.99.0                        

• Switched to the new knncolle C++ libaries for all implementations. This greatly streamlines the internals and allows downstream packages to re-use the search indices in their own C++ code.

• Parallelization is now performed using the standard <thread> library. This avoids the overhead of forking or starting new processes via BiocParallel.

• All *Index classes have been removed. The output of buildIndex() is no longer guaranteed to be serializable, e.g., external pointers to C++-owned objects; attempting to do so will raise a “null pointer to prebuilt index” error for all methods implemented in this package. The removal of this guarantee makes it easier to extend BiocNeighbors to new methods where the index structure does not have an obvious R representation.

• All functions (findKNN(), queryNeighbors(), etc.) will no longer coerce X to a matrix, to avoid the headache of S4 dispatch ambiguity. Users should coerce their data into matrix format before supplying it to these functions.

• The last= option in findKNN() and queryKNN() has been replaced by the findDistance() and queryDistance() functions instead. This provides a much more intuitive method for the typical use of last=, i.e., to obtain the distance to the k-th nearest neighbor.

• findNeighbors() no longer reports each point as its own neighbor. Also, all neighbors are now sorted by increasing distance in findNeighbors() and queryNeighbors().

BiocSingular

                   Changes in version 1.22.0                        

• Bugfix for scale=TRUE with zero-variance rows.

biomaRt

                   Changes in version 2.62.0                        

USER VISIBLE CHANGES

• Several deprecated functions are now defunct.

BUG FIXES

• Results returned from BioMart queries will be read using Latin-1 encounding if the default fails. Reported in https://support.bioconductor.org/p/9158844/ (Backported to 2.60.1)

• Fixed issue when only one dataset was listed in a Mart instance, causing data.frame dimensions to be dropped. This broke connectivity to https://parasite.wormbase.org. (Backported to 2.60.1)

BioNAR

                     Changes in version 1.7                         

• Add function to calculate the BowTie decomposition of the graph.

Biostrings

                   Changes in version 2.74.0                        

NEW FEATURES

• Add ellipsis to arg list of matchProbePair() generic and methods. Extra arguments passed thru the ellipsis are forwarded to the internal calls to matchPattern(). [by Aidan Lakshman <ahl27@pitt.edu>]

SIGNIFICANT USER-VISIBLE CHANGES

• Undeprecate longestConsecutive().

• A warning in translate() has been elevated to an error because AA_ALPHABET is now enforced. [by Aidan Lakshman <ahl27@pitt.edu>]

• man/XStringSetList-class.Rd previously said that “DNAStringSetList and AAStringSetList are the only constructors”, but the current version of Biostrings includes BStringSetList and RNAStringSetList constructors. This has been updated. [by Aidan Lakshman <ahl27@pitt.edu>]

BUG FIXES

• replaceAmbiguities() now checks to ensure input is DNA or RNA. This previously caused some odd behavior with AA input. [by Aidan Lakshman <ahl27@pitt.edu>]

• Fix bug in consensusMatrix() when input has length zero. [by Aidan Lakshman <ahl27@pitt.edu>]

• Get rid of spurious warning in readQualityScaledDNAStringSet(). [by Aidan Lakshman <ahl27@pitt.edu>]

bluster

                   Changes in version 1.16.0                        

• Add num.threads= to all neighbor-based methods, to be passed to BiocNeighbors.

• Parallelize the SNN graph construction in makeSNNGraph().

BREW3R.r

                    Changes in version 1.1.1                        

• Fix case when the input_gr_to_overlap have both stranded intervals and unstranded intervals (the users were facing a Warning but the results was not the expected one).

BSgenome

                   Changes in version 1.74.0                        

• No significant changes in this version.

BSgenomeForge

                    Changes in version 1.6.0                        

• No significant changes in this version.

bsseq

                    Changes in version 1.41                         

• Changing saveRDS to base::saveRDS following upstream changes.

bugsigdbr

                   Changes in version 1.11.4                        

• Update stable release version for data on Zenodo

CAGEr

                   Changes in version 2.12.0                        

BACKWARDS-INCOMPATIBLE CHANGES

• The range argument of the annotateCTSS function is renamed annot.
• The removeSingletons option of clustering methods is removed and the default value of keepSingletonsAbove is set to 0, which keeps the standard behavior.
• In cluster objects, the dominant CTSS score is now stored in the dominantCTSS object directly.
• The clusterCTSS function is replaced by the new paraclu and distclu function. CTSS filtering is done beforehand with the new filterLowExpCTSS function.
• Removed CTSSclusteringMethod() function and stop recording clustering method name.
• Removed returnInterquantileWidth argument of functions and always return that width when quantile information is provided. Closes #114
• The CTSStagCountDA function is removed.
• The dominant peak in TagClusters objects is now a GRanges object like in ConsensusClusters.
• The custom method for tag clustering is removed. It was obsoleted by the newer CustomConsensusClusters function.
• The exportToTrack function now exports scores of tag clusters and consensus clusters instead of setting them to zero.

NEW FEATURES

• Support the use of TxDB objects for annotating clusters.
• The plotReverseCumulatives() function now uses ggplot2. Its main, legend, xlab, ylab, xlim and ylim arguments were removed as this can be controlled via ggplot2 functions.
• New TSSlogo function wrapping the ggseqlogo package.
• New distclu and paraclu functions that can run directly on CTSS objects. You can use them to test parameters before running the whole CAGEexp object through clusterCTSS.

BUG FIXES

• CTSS filtering now works correctly with threshold = 0, thresholdIsTpm = TRUE.
• The importPublicData function was repaired for FANTOM samples.
• Remove broken and obsolete customClusters method of clusterCTSS. Use CustomConsensusClusters() instead. Fixes #113.
• Ensure consensus clusters can be exported as tracks with interquantile width information. Fixes #108, #70.

OTHER CHANGES

• Accelerated the computation of cumulative sums ~10×.
• Singleton filtering is now done by the paraclu and distclu functions themeselves; .ctss_summary_for_clusters does not change the input clusters except for adding information.

Cardinal

             Changes in version 3.7.8 (2024-10-26)                  

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecate ‘slice()’ in factor of ‘sliceImage()’ to avoid conflicts with users attaching dplyr

             Changes in version 3.7.7 (2024-10-24)                  
  

SIGNIFICANT USER-VISIBLE CHANGES

• Update ‘peakAlign()’ with ‘binratio’ parameter

             Changes in version 3.7.6 (2024-10-16)                  
  

NEW FEATURES

• Reading/writing imzML now preserves ‘metadata’ slot

• Reading/writing imzML now supports parallel processing

SIGNIFICANT USER-VISIBLE CHANGES

• Update ‘estimateDomain()’ to select resolution based on ‘median’, ‘min’, ‘max’, or ‘mean’

• Update ‘peakAlign()’ to build domain bins based on the minimum of peak gaps (instead of the median)

• Write log file when writing imzML/Analyze files

BUG FIXES

• Fix bug in ‘process()’ resulting in output matrix with ‘list’ elements under certain conditions

                    Changes in version 3.7.5                        
  

NEW FEATURES

• Add ‘setCardinalParallel()’ for setting a parallelization backend with reasonably-selected defaults

SIGNIFICANT USER-VISIBLE CHANGES

• Add ‘SAR=FALSE’ option to ‘simulateImage()’ for faster simulation if spatial autoregressive model is not needed

• Change default array order for ‘MSImagingArrays’ so that ‘intensity’ is first array and ‘mz’ is second array

• Improved logging with pre-processing functions

BUG FIXES

• Fix leaky ‘meansTest()’ closures

                    Changes in version 3.7.4                        
  

NEW FEATURES

• Add ‘saveCardinalLog()’ for saving log file

• Add ‘getCardinalLogger()’ + ‘setCardinalLogger()’

• Add ‘fetch()’ and ‘flash()’ methods for moving spectra between shared memory and temporary files

SIGNIFICANT USER-VISIBLE CHANGES

• Update compatibility with matter 2.7.6

• Changes to ‘simulateSpectra()’ and ‘simulateImage()’ in parallelization and spectral noise generation

• RNG in ‘simulateSpectra()’ and ‘simulateImage()’ now warn if ‘RNGkind()’ is not “L’Ecuyer-CMRG”

BUG FIXES

• Fix calculation of “adaptive” spatial weights in ‘spatialWeights()’ for accuracy and stability

                    Changes in version 3.7.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Add ‘setCardinalChunksize()’ + ‘getCardinalChunksize()’

• Update vignettes due to spectral processing updates

BUG FIXES

• Fix plot() and image() not always respecting dimnames

• Fix plot() and image() not plotting multiple columns

• Fix plot() and image() failing for non-syntactic names

                    Changes in version 3.7.2                        
  

BUG FIXES

• Merge bug fix from 3.6.4.

                    Changes in version 3.7.1                        
  

NEW FEATURES

• Update ‘spectrapply()’ so index array is optional

• Update ‘plot()’ to support 2 domains (e.g., for ion mobility)

• Add plotting methods for ‘XDataFrame’ and ‘PositionDataFrame’

BUG FIXES

• Fix default ‘tolerance’ in ‘pixels()’

                    Changes in version 3.6.6                        
  

BUG FIXES

• Fixes for ‘simulateImage()’ and ‘simulateSpectra()’

                    Changes in version 3.6.5                        
  

BUG FIXES

• Fix ‘spatialShrunkenCentroids()’ failing when ‘r=0’ or when a pixel has no neighboring pixels

                    Changes in version 3.6.4                        
  

BUG FIXES

• Bug fixes for ‘plot()’ on spectra with queued processing

                    Changes in version 3.6.3                        
  

BUG FIXES

• Bug fixes for ‘meansTest()’ when random effects are specified

                    Changes in version 3.6.2                        
  

BUG FIXES

• Version bump for ‘matter’ 2.6.2 bugfixes

                    Changes in version 3.6.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Add ‘mass.range’ and tolerance’ arguments to ‘bin()’

BUG FIXES

• Fix ‘readImzML’ error if imzML fails conversion to ‘ImzMeta’

CardinalIO

             Changes in version 1.3.6 (2024-10-24)                  

BUG FIXES

• Fix writing scientific notation to imzML output (note: only affected parsing, not precision)

             Changes in version 1.3.5 (2024-10-16)                  
  

NEW FEATURES

• Support for parallel writing with BiocParallel

• Added ‘BPPARAM’ argument to ‘writeAnalyze()’

• Added ‘BPPARAM’ argument to ‘writeImzML()’

SIGNIFICANT USER-VISIBLE CHANGES

• Return ‘outdata’ attribute on ‘writeAnalyze()’ results with output ‘matter’ object

• Return ‘outdata’ attribute on ‘writeImzML()’ results with output ‘matter’ object

                    Changes in version 1.3.4                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Parse imzML “binary data compression type” tags

• Compressed ibd data arrays are now attached as raw byte arrays (without decompression)

                    Changes in version 1.3.3                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Changed default ‘mz.type’ from “float32” to “float64”

                    Changes in version 1.3.2                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Renaming imzML files when ‘asis=TRUE’ now signals a warning

                    Changes in version 1.3.1                        
  

BUG FIXES

• Update broken unit test to reflect recent changes in ‘matter’

                    Changes in version 1.2.1                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Allow multiple options to ‘check’ in ‘parseImzML’

BUG FIXES

• Check ibd file size against imzML binary data array offsets

cbaf

             Changes in version 1.28.0 (2024-10-24)                 

New Features

• Introducing a new two step procedure for processMultipleStudies! If you intend to download the required data on server, CBAF can download and create a database, then it compress the database into a ZIP file. User can then transfer the zipped file into their local computer and CBAF can use that ZIP file to recreate the intial database that it needs. Since servers usually lack any graphical units, CBAF won’t be able to generate heatmaps when running on server.

cellxgenedp

                    Changes in version 1.10                         

SIGNIFICANT USER-VISIBLE CHANGES

• (v.1.9.1) Add progress bar when updated db()

ChIPpeakAnno

                   Changes in version 3.39.3                        

• Fix the documentation for Vennerable.

                   Changes in version 3.39.2                        
  

• Fix the documentation for summarizePatterInPeaks.

                   Changes in version 3.39.1                        
  

• Unique promoters for genomicElementDistribution.

ChIPseeker

                   Changes in version 1.41.3                        

• Better covplot(). Support universal chromosome names, and keep the default order of multiple peaks when plot a list of GRanges object.
• Robust generate_colors(). Edit the logical of decision, and can validate color code automatically.

• Extend dplyr verbs (filter(), mutate(), arrange(), rename()) to peak (GRanges object or data.frame), see #242.

                   Changes in version 1.41.2                        
  

• Enhancement of plotDistToTSS(), see #241.

                   Changes in version 1.41.1                        
  

• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)

ClassifyR

                   Changes in version 3.10.0                        

• Metric calculation done at fold level rather than permutation level.

clusterProfiler

                   Changes in version 4.13.4                        

• re-export DOSE::enrichDO() and DOSE::gseDO() (2024-10-01, Tue)

                   Changes in version 4.13.3                        
  

• fixed bug in enrichPC() (2024-08-26, Mon)

                   Changes in version 4.13.2                        
  

• fixed bug of gson_KEGG() (2024-08-19, Mon)

                   Changes in version 4.13.1                        
  

• update functions to access PathwayCommons data (2024-08-11, Sun, gson#9)
• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)
• update kegg_category information (7 categories and 572 subcategories) (2024-07-26, Fri)
• Cellular Processes (36)
• Drug Development (75)
• Environmental Information Processing (41)
• Genetic Information Processing (39)
• Human Diseases (99)
• Metabolism (190)
• Organismal Systems (92)

ClustIRR

                   Changes in version 1.3.34                        

• Stable version but not tested

                   Changes in version 1.3.25                        
  

• Major changes since this version including
  • community detection
  • Stan model-based differential community occupancy

  • supporting functions

                   Changes in version 1.3.20                        
    

• Future based parallelization in clustering and graphing

                    Changes in version 1.3.1                        
  

• Stub functions for integration of data from VDJdb, TCR3d and MCPAS-TCR

ComplexHeatmap

                   Changes in version 2.21.1                        

• pheatmap(): na_col is passed to Heatmap().

CompoundDb

                     Changes in version 1.9                         

Changes in version 1.9.5

• Add new extractByIndex() method.

Changes in version 1.9.4

• compound_tbl_lipidblast supports now parallel processing and extracts more information from MoNA’s JSON format (thanks to Prateek Arora for contribution).

Changes in version 1.9.3

• compound_tbl_lipidblast: ensure exactmass is of type numeric.

Changes in version 1.9.2

• compound_tbl_lipidblast: add parameter n to support reading and processing MoNA json files in sets (chunks) of lines at a time and hence reduce memory demand for very large files.

Changes in version 1.9.1

• Allow CompDb to store that database name as alternative to an active database connection. This allows to serialize and load an object to/from disk (serializing an active database connection would not be possible) . Each call to extract data from the database will however open (and close) its own connection.

COTAN

                   Changes in version 2.5.11                        

Fixed bug in the function cellsUMAPPlot(): restored possibility of passing a genes vector as genesSel parameter. Also updated the documentation about the available genes selection methods

                   Changes in version 2.5.10                        

Fixed typo in error message

Fixed bug in function genesCoexSpace(): now primaryMarkers can have only a single gene

                    Changes in version 2.5.9                        

Exported utility functions about names arrays: conditionsFromNames(), niceFactorLevels(), factorToVector()

                    Changes in version 2.5.8                        

feature/add_condition_arguments_to_plot_functions Now the following plot functions take in conditions explicitly, instead of just instructions to determine them from the cells’ names. The changes involved: cellSizePlot(), ECDPlot(), genesSizePlot(), mitochondrialPercentagePlot(), scatterPlot()

Added possibility to convert COTAN objects to/from SingleCellExperiment objects. SCE objects created by the Seurat package are supported

Hardened arguments’ checks for function UMAPPlot()

Solved issue with the function establishGenesClusters(): it was throwing an error when one of the sub-lists in the groupMarkers argument did contain only one element

                    Changes in version 2.5.7                        

Introduced new way to check for the Uniform-Transcript property of the clusters based on multiple thresholds calibrated so that the new method is more effective at describing really statistically uniform clusters

Functions cellsUniformClustering() and mergeUniformCellsClusters() have been re-factored so to support new class hierarchy for UT checkers. This allows user to select which method to use for the checks; as of now the following methods are supported:

• “SimpleGDIUniformityCheck”
• “AdvancedGDIUniformityCheck”

Avoided issue with pdf file creation: file handle was not closed in case of errors

Added possibility of choosing number of features in seuratHVG()

Solved minor issue with with clusterization functions in cases when only one cluster was created

                    Changes in version 2.5.6                        

Made function heatmapPlot() more easy to use and in line with the rest of the COTAN package

Now the method storeGDI() can take in the output data.frame from the function calculateGDI()

Solved few minor issues with the vignette and changed a few default parameters in cellsUMAPPlot(), pValueFromDEA() and findClustersMarkers()

                    Changes in version 2.5.5                        

Stopped function cellsUniformClustering() from saving the internally created Seurat object due to possibly long saving times

Split the now deprecated function getNormalizedData() into two separated functions: getNuNormData() and getLogNormData()

Re-factored function mergeUniformCellsClusters() to be more precise: now it merges clusters starting from the most similar in latest batch and also runs the merging in multiple steps adjusting gradually the GDI threshold ranging from a very strict up to the user given ones.

Fixed minor bugs in functions GDIPlot() and clustersMarkersHeatmapPlot()

                    Changes in version 2.5.4                        

Added possibility to display UMAP plots of cells clusters, using the function cellsUMAPPlot()

                    Changes in version 2.5.3                        

Updated the vignette to the most recent changes

Allowed user to set the ratio of genes above the threshold allowed in a Uniform Transcript cluster

                    Changes in version 2.5.2                        

Solved issue with usage checks about the torch library

Allowed user to explicitly opt-out from the torch library usage: COTAN will avoid torch commands when the option “COTAN.UseTorch” is set to FALSE

                    Changes in version 2.5.1                        

Added support for the torch library to help with the heavy lifting calculations of the genes’ COEX matrix, with consequent substantial speed-up, especially when a GPU is available on the system

                    Changes in version 2.5.0                        

First release in Bioconductor 3.20

cqn

                    Changes in version 1.51                         

• Various small changes addressing changes in dependencies. For example, decideTestsDGE got renamed to decideTests. Likewise, a number of imports needed fixing.

crisprBase

                    Changes in version 1.9.1                        

• Added Csm complex RNA-targeting nuclease.

crisprDesign

                    Changes in version 1.7.1                        

• Fixed getTssObjectFromTxObject for negative strand.

crisprScore

                    Changes in version 1.9.3                        

• Fixed documentation for enPamGB and DeepCpf1 algorithms.

                    Changes in version 1.9.2                        
  

• Fixed python environments based on the lastest changes in basilisk (using conda-forge installations).

CTdata

                     Changes in version 1.5                         

CTdata 1.5.3

• Correction of a bug in mean_methylation_in_embryo and mean_methylation_in_FGC datasets
• Vignette update

CTdata 1.5.2

• Correction of an error in the upload

CTdata 1.5.1

• Used more stringent threshold to define genes activated in CCLE cell lines ang in TCGA tumors (TPM > 1 in at least 1% of tumors and cancer cell lines, and TPM > 5 in at least one tumor and cancer cell line)
• Changed selection criteria of testis-specific and testis-preferential genes in GTEX
• Added a slightly more stringent criteria of selection of testis-specific genes when analysing RNAseq data of normal tissues with multimapping
• Minor modifications in selection of genes induced by DAC
• Set TCGA_catgeory in TCGA_TPM to “leaky” when the q75 expression in normal peritumoral TCGA samples is higher than 0.5
• Added HPA_cell_type_specificity (a table giving cell type specificity of each genes based on Human protein Atlas scRNAseq data)
• Added FGC_sce, scRNAseq data of human fetal gonads
• Added oocytes_sce, scRNAseq data of human oocytes
• Changed preliminary CT_list into all_genes_prelim list to add the characterisation to all genes and not only CT in the package
• Changed criteria for testis specificity, including HPA/TCGA/CCLE category in the definition
• Added CT_gene_type column to differentiate CT genes and CT preferential genes
• Included all genes in methylation objects (methylation_in_tissues, mean_methylation_in_tissues and TCGA_methylation)
• Added all_genes containing all the characterisation and analysis for all genes
• Changed the criteria for regulation by methylation, needing DAC induction and methylation in somatic only
• Reordered CT_genes and all_genes
• Changed all documentation
• Added embryo, FGC and hESC data

CTdata 1.5.0

• New devel

CTexploreR

                     Changes in version 1.1                         

CTexploreR 1.1.3

• Add pkgdown config.
• Correcting typo in fetal_germcells_mean_methylation() function name
• Adding tests for new functions

CTexploreR 1.1.2

• Created functions to visualise expression in fetal germ cells, oocytes, hESC and early embryos.
• Created functions to visualise methylation in fetal germ cells, hESC and embryo.

CTexploreR 1.1.1

• Adaptation due to updates in CTdata : adding all genes to functions, choice to include CT preferential.

CTexploreR 1.1.0

• New devel

cydar

                   Changes in version 1.30.0                        

• Updated to use the latest BiocNeighbors, which means that the output of prepareCellData() is no longer serializable. This is because the precomputed index is now an external pointer to a C++-owned data structure, and cannot be moved between sessions. (Arguably, it was a mistake to expose these internals in the expected workflow for this package, but that ship has sailed.) Hopefully, this should not affect most users as they should be primarily interacting with the CyData object.

cypress

             Changes in version 1.1.1 (2024-05-27)                  

• Reduce dependent packages

• Revise the rd file

CytoMDS

                     Changes in version 1.1                         

CytoMDS 1.1.4

• implemented pkgdown customization

CytoMDS 1.1.2 & 1.1.3

• expression matrices as input to EMD calculation

CytoMDS 1.1.1

• added citation to bioRxiv pre-print

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

CytoPipeline

                     Changes in version 1.5                         

CytoPipeline 1.5.2

• updated unit test to account for flowAI version change
• now suggesting CytoPipelineGUI package

CytoPipeline 1.5.1

• updated processing step argument matching using phenoData

CytoPipelineGUI

                     Changes in version 1.3                         

CytoPipelineGUI 1.3.1

• implemented pkgdown site customization

dar

                    Changes in version 1.1.2                        

Bug Fixes

• data_import.Rmd

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”)

DegCre

                    Changes in version 1.1.1                        

• Version up.

                 Changes in version 1.1.0.9000                      
  

NEW FEATURES

• runDegCre now accepts “qvalue” as an input to pAdjMethod which is now the default. Our testing shows that this method improves the performance of DegCre predictions. The qvalue calculation does not require the user to specify a alphaVal.

• Added new function collapseDegCreToGene which converts DegCre results for gene with multiple TSSs to use only the association that spans the shortest distance.

• Added new function calcAssocProbOR that calculates the odds-ratio for DegCre association probabilities. This function can operate on assocProb or rawAssocProb values by altering the type flag. It is meant to replace calcRawAssocProbOR.

• Added new function convDegCreResListToCreGeneScoreGR that converts DegCre results to a simplified GRanges with the predicted gene and score as metadata.

OTHER CHANGES

• Streamlined runDegCre code to use more subfunctions.

BUG FIXES

• Changed the internal function makePlotGInter to return a sorted GInteractions to avoid inconsistent returns.

                    Changes in version 1.0.2                        
  

• Changed citation to Genome Research article

BUG FIXES

• Added parameter minNDegs to optimizeAlphaDegCre to stop it from trying testedAlphaVals that result in the number of passing DEGs to be too low for the optimization algorithm to function properly.

DEGreport

                   Changes in version 1.41.1                        

• made that the sequence of clusters in the dendogram matches the sequence of clusters in the trajectories @zellerivo

• Fix error in check report about stack limit size

• Add option to avoid running dendextend https://github.com/lpantano/DEGreport/issues/62

DelayedArray

                   Changes in version 0.32.0                        

NEW FEATURES

• Add nzwhich() method for DelayedArray objects (block-processed).

• Support %*%, crossprod(), and tcrossprod() between DelayedMatrix and COO_SparseMatrix objects.

SIGNIFICANT USER-VISIBLE CHANGES

• The default realize() method now returns an SVT_SparseArray object instead of an SparseArraySeed object when the array-like object to realize is sparse and ‘BACKEND’ is NULL.

• Coercing a DelayedArray object or derivative to SparseArray should be much more efficient (thanks to various tweaks that happened in the SparseArray and HDF5Array packages).

DEPRECATED AND DEFUNCT

• Deprecate SparseArraySeed objects.

• Deprecate OLD_extract_sparse_array() and read_sparse_block() generics and methods.

• Fix bug in coercion from DelayedArray to SparseArray when the object to coerce has NAs. See https://github.com/Bioconductor/HDF5Array/issues/61

DelayedMatrixStats

                    Changes in version 1.27                         

• Remove colAnyMissings() and rowAnyMissings(), which were deprecated in Version 1.23 and made defunct in Version 1.25.

demuxSNP

                    Changes in version 1.4.0                        

Added reassign_centroid() function for improved handling of sparse and missing data. Added messaging to previous functions reassign(), reassign_jaccard() and reassign_balanced() to point towards reassign_centroid(). Updated add_snps() function to add unfiltered data.

DepecheR

             Changes in version 1.21.4 (2024-08-22)                 

• Minor bug fixes in neighSmooth.

             Changes in version 1.21.3 (2024-06-21)                 
  

• Minor bugs in depeche affecting the special case of one defining marker and two clusters.

             Changes in version 1.21.2 (2024-06-14)                 
  

• Correction of the number of used neighbors in neighSmooth function.

DESeq2

                   Changes in version 1.45.1                        

• Dropping the requirement for DESeqDataSet to contain integers. This allows fitType=”glmGamPoi” to be used. If non-integer counts are present and other fitType values are provided, the various functions will give an error, e.g. DESeq, estimateDispersions, nbinomWald, and nbinomLRT. To avoid integer conversion, use DESeqDataSet() with skipIntegerMode=TRUE. For more detail see: https://github.com/thelovelab/DESeq2/issues/66

DNABarcodeCompatibility

             Changes in version 1.21.1 (2024-09-18)                 

• Addition of the distance() function from the DNABarcodes package

DOSE

                   Changes in version 3.99.1                        

• return NULL in GSEA if not genes can be mapped (2024-08-26, Mon, ReactomePA#43)

                   Changes in version 3.31.4                        
  

• remove mpoSim() and hopSim() (2024-08-21, Wed)

                   Changes in version 3.31.3                        
  

• remove gseMPO() and gseHPO(), instead using e.g., gseDO(ont=”HPO”) (2024-08-15, Thu)
• remove enrichMPO() and enrichHPO(), instead using e.g., enrichDO(ont=”HPO”)
• unify API and removing the usages of MPO.db and HPO.db
• update DO-gene mapping data (2024-08-13, Tue)
• remove HDO.db and use new API in GOSemSim (v>=2.31.1) (2024-08-13, Tue)

• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)

                   Changes in version 3.31.2                        
  

• add FoldEnrichment, RichFactor and zScore in ORA result (2024-06-13, Thu)

                   Changes in version 3.31.1                        
  

• fixed bug in options(enrichment_force_universe=TRUE) (2024-05-16, Thu) - https://github.com/YuLab-SMU/clusterProfiler/issues/283#issuecomment-2077869230

dreamlet

                    Changes in version 1.3.3                        

• July 19, 2024
• fix in .read_matrix_block()

• See https://github.com/GabrielHoffman/dreamlet/pull/23/commits/c453ac98ebc0329279b4dd3ae26a674df0e9b1f2

                    Changes in version 1.3.1                        
  

• May 31, 2024
• bump Bioc version

easyRNASeq

                   Changes in version 2.41.1                        

• Ported changes from 2.40.1

                   Changes in version 2.40.1                        
  

• Fixed broken dependencies (Biostrings::type is now BiocGenerics::type and BiocGenerics::clusterApply is now parallel::clusterApply).

• Adapted to changes for Roxygen

• Changed from using biomaRt::useMart to biomaRt::useEnsembl

edgeR

             Changes in version 4.4.0 (2024-10-30)                  

• New function catchRSEM() to read transcript-level quantifications from RSEM output. If the RSEM output includes resampling replicates, then catchRSEM() uses them to estimate the over-dispersion arising from read-to-transcript-ambuity for each transcript. Similar to catchSalmon() and catchKallisto() but for RSEM output.

• New function normalizeBetweenArrays.DGEList() to apply microarray-style normalization to a DGEList by setting the offset matrix appropriately.

• New argument keep.unit.mat for glmQLFit(). The unit matrices produced when ‘legacy=FALSE are not required for routine downstream analysis, so they are now not returned by glmQFit() unless keep.unit.mat=TRUE`. This reduces the size of the glmQLFit fitted model object.

• Output components var.prior and var.post from glmQLFit() have been renamed to s2.prior and s2.post.

• glmQLFit() with legacy=FALSE now uses the improved empirical Bayes hyperparameter estimation in limma 3.61.9, which is designed especially for scenarios when the residual degrees of freedom are unequal between genes. Now that unequal residual df are better accounted for, very small df.residual values are no longer floored to zero before performing empirical Bayes estimation.

• The default value of top.proportion in glmQLFit() with legacy=FALSE now depends on the number of genes and on the residual degrees of freedom, with more genes and more df giving smaller values. Also, the DGEList method for glmQLFit() with legacy=FALSE will take the dispersion from the mean of the right tail values of the trended dispersions, instead of re-estimating, if these are found in the DGEList object.

• makeCompressedMatrix() now allows x to optionally be a row vector (matrix with one row) or a column vector (matrix with one column) or an ordinary vector. Previously, matrix values for x were simply returned as output.

• diffSpliceDGE() now passes weights to glmFit.default(), if they exist.

• A major revision has been undertaken to the C source code. C++ has been removed in favor of pure C and, instead, the C functions are now wrapped into R in modern style. edgeR no longer depends on the Rcpp package. The new C code includes careful memory management and a simplified file structure.

• Various edits to help pages. The edgeR publications in edgeR-package.Rd are now listed in reverse chronological order. Some help page cross-references have been fixed. The term “scalar” to indicate a numeric vector of length one has been replaced with “single value” in several places. The DGEGLM and glmFit help pages now clarify that the output coefficients component is on the natural log scale.

• Add checks for negative or NA counts to cpm(), cpmByGroup() and normLibSizes().

• Minor R code improvements that do not change the user interface to various functions, for example replacing any(is.na()) with anyNA() and using identical() when testing conditions within if() statements.

• Remove decidetestsDGE(), whose functionality is now provided by the generic function decideTests().

enrichplot

                   Changes in version 1.25.6                        

• pretty gene count legend (2024-10-29, Tue, #271)

                   Changes in version 1.25.5                        
  

• new emaplot(), goplot(), cnetplot() and ssplot(), all power by ‘ggtangle’ package (2024-10-24, Thu)
• re-export ggtangle::cnetplot() (2024-10-24, Thu)

• remove drag_network() (2024-10-24, Thu)

                   Changes in version 1.25.4                        
  

• fixed goplot() (2024-10-23, Wed, #297, #732, #718)

                   Changes in version 1.25.3                        
  

• hplot(): Horizontal plot for GSEA result (2024-08-27, Tue)

                   Changes in version 1.25.2                        
  

• fixed bug in ridgeplot() (2024-08-19, Mon, clusterProfiler#704)

                   Changes in version 1.25.1                        
  

• fixed GeneRatio in dotplot as character of fraction issue (2024-08-16, Fri, clusterProfiler#715)
• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)
• dotplot2 to compare two selected clusters in ‘compareClusterResult’ object (2024-06-15, Sat)
• volplot to visualize ORA result using volcano plot (2024-06-13, Thu)

enrichViewNet

                    Changes in version 1.3.4                        

NEW FEATURES

• The ‘force’ parameter in createEnrichMapMultiComplex() has been removed.

• The ‘force’ parameter in createEnrichMapMultiBasic() has been removed.

• The ‘force’ parameter in createEnrichMap() has been removed.

                    Changes in version 1.3.3                        
  

NEW FEATURES

• The createEnrichMapMultiComplex() now has an new parameter … that enables passing extra parameters to imbedded emapplot() function.

• The createEnrichMapMultiBasic() now has an new parameter … that enables passing extra parameters to imbedded emapplot() function.

• The createEnrichMap() now has an new parameter … that enables passing extra parameters to imbedded emapplot() function.

                    Changes in version 1.3.2                        
  

BUG FIXES

• The package uses the Ensembl list rather than the query list to extract information when intersection column is missing, in the extractInformationWhenNoIntersection() function.

                    Changes in version 1.3.1                        
  

BUG FIXES

• The package uses the information about the organism when querying the gprofiler database.

ensembldb

                   Changes in version 2.29.1                        

• Improve documentation of proteinToGenome() and require named IRanges as input to proteinToGenome().

epialleleR

             Changes in version 1.13.4 (2024-10-10)                 

• VariantAnnotation moved to Suggests

             Changes in version 1.13.3 (2024-10-04)                 
  

• plotPatterns for pretty plotting

EpiCompare

                    Changes in version 1.9.5                        

New features

• Remove the soon-to-be-deprecated BRGenomics dependency.
• Port tidyChromosomes function to EpiCompare.

Miscellaneous

• Update maintainer details.

epiregulon.extra

                    Changes in version 1.0.1                        

fixed documentation for plotHeatmapActivity fixed legend label of summary.logFC in plotBubble removed duplicate genes from plotHeatmapRegulon

erccdashboard

                   Changes in version 1.39.5                        

• Depends on R > 4.0

• Converted from Sweave PDF vignette to Rmarkdown HTML.

• Updating testDECount.R to handle changes made in edgeR

• Updating saveERCCPlots.R to deal with grob error

escape

             Changes in version 2.1.5 (2024-10-23)                  

• update handling of v5 Seurat versus <v5 Seurat Objects

             Changes in version 2.1.4 (2024-09-13)                  
  

• update densityEnrichment() GSVA function pull

             Changes in version 2.1.3 (2024-09-13)                  
  

#VERSION BUMP FOR BIOCONDUCTOR

UNDERLYING CHANGES

• update densityEnrichment() for new GSVA function name
• Parallelization of performNormalization()

• Refactor of getGeneSets() to prevent issues with m_df error.

             Changes in version 2.0.1 (2024-07-26)                  
  

UNDERLYING CHANGES

• fixed performNormalziation() errors when input.data was a matrix, now requires single-cell object and enrichment data
• passing parallel processing properly to runEscape() function.

EWCE

                   Changes in version 1.13.1                        

Bug fixes

• Making ewce_plot functionality more clear - will no fail if make_dendro=TRUE and ggdendro is not installed or CTD is not provided rather than issuing a warning.

ExperimentHub

                   Changes in version 2.13.0                        

BUG FIXES

• (2.13.1) merged @votti PR for not checking connection if localhub is selected

extraChIPs

                    Changes in version 1.9.6                        

• Added the function centrePeaks() to recentre peaks using any files with coverage

faers

                    Changes in version 1.1.6                        

• fda_drugs() now directly use a fixed url to download the data

• faers_meta(internal = TRUE) will always use the cache data in the package.

• Rename “gndr_cod” into “gender” for periods before 2014q2, and rename “sex” into “gender” for periods after or equal to 2014q2.

• “sex” was added, which recoded any values other than “F” or “M” as NA.

                    Changes in version 1.1.4                        
  

• fix error when download failed

• meddra augment additional argument primary_soc to help save the full meddra data

fenr

                    Changes in version 1.2.1                        

• Go term namespace added to the information extracted by fetch_go.

fgsea

                   Changes in version 1.31.6                        

• plotCoregulationSpatial supports multiple samples

                   Changes in version 1.31.3                        
  

• check for empty strings in gene names

• minor fix in leading edge calculation

                   Changes in version 1.31.2                        
  

• fora() provides fold enrichment scores for more effective prioritisation of results

flowAI

                   Changes in version 1.35.2                        

• Substantial modification of the anomaly detection in the flow rate. Added a parameter to remove parts of the flow rate from the mode. Added the Loess regression as alternative method. Removed the deviationFR parameter.

fmrs

                    Changes in version 2.0.1                        

IMPROVEMENTS SINCE LAST RELEASE

• Non-mixture of regression models are now added to the package.

BUG FIXES

• Several bugs are fixed.

                    Changes in version 2.0.0                        
  

IMPROVEMENTS SINCE LAST RELEASE

• The package is rewritten using .Call function.
• The codes for Weibull distribution are improved.

BUG FIXES

• Several bugs are fixed which caused the results to be different for the same analysis.

fobitools

                   Changes in version 1.13.1                        

• Fix bugs in vignettes

gDRcore

           Changes in version 2024-10-24 (2024-10-24)               

• split and refactor annotation functions

           Changes in version 2024-10-21 (2024-10-21)               
  

• add support for reprocessing data with old data model

           Changes in version 2024-09-30 (2024-09-30)               
  

• handle properly additional perturbations to get rid of creating additional columns that can’t be hangle properly by the app

           Changes in version 2024-08-21 (2024-08-21)               
  

• identify additional perturbations hidden in the secondary drug

           Changes in version 2024-08-19 (2024-08-19)               
  

• utilize calc_sd function

           Changes in version 2024-08-09 (2024-08-09)               
  

• fix issue with wrong mapping of Day0 data

           Changes in version 2024-08-08 (2024-08-08)               
  

• fix issue with mapping overrides untreated controls

           Changes in version 2024-08-05 (2024-08-05)               
  

• fix issue with non-avearaged concentration data

           Changes in version 2024-07-23 (2024-07-23)               
  

• fix issue with providing empty nested_confounder

           Changes in version 2024-07-17 (2024-07-17)               
  

• allow using custom functions for calculating HSA and Bliss scores for combination data

           Changes in version 2024-07-15 (2024-07-15)               
  

• refactor logic for calculating standard deviation for single values

           Changes in version 2024-07-10 (2024-07-10)               
  

• update unit tests

           Changes in version 2024-06-04 (2024-06-04)               
  

• switch to get_supported_experiments

gDRimport

           Changes in version 2024-10-22 (2024-10-22)               

• fix test for load_files

           Changes in version 2024-08-29 (2024-08-29)               
  

• fix failing github page

           Changes in version 2024-08-12 (2024-08-12)               
  

• update function for importing public PRISM data

           Changes in version 2024-07-03 (2024-07-03)               
  

• fix a bug with incorrect recognition of input file types

gDRstyle

           Changes in version 2024-08-29 (2024-08-29)               

• add GitLab credentials to pkgdown builds

           Changes in version 2024-06-10 (2024-06-10)               
  

• add debug to the exceptions list

gDRutils

           Changes in version 2024-10-11 (2024-10-11)               

• make duplicates’ helpers supporting combo assays as well

           Changes in version 2024-10-07 (2024-10-07)               
  

• refactor the logic for dealing with duplicates in assay data

           Changes in version 2024-10-03 (2024-10-03)               
  

• fixed issue in average_biological_replicated (fit_type)

           Changes in version 2024-09-16 (2024-09-16)               
  

• add functions set_unique_cl_names_dt and set_unique_drug_names_dt

           Changes in version 2024-09-04 (2024-09-04)               
  

• remove hack with checkDimnames

           Changes in version 2024-08-30 (2024-08-30)               
  

• remove GDS fit_source from gDRviz

           Changes in version 2024-08-28 (2024-08-28)               
  

• extend the logic of get_additional_variables to support other sources of fitting metrics

           Changes in version 2024-08-14 (2024-08-14)               
  

• extend the logic of average_biological_replicates_dt to calculate standard deviation

           Changes in version 2024-08-06 (2024-08-06)               
  

• add functions for setting unique identifiers in the colData and rowData of SE

           Changes in version 2024-07-30 (2024-07-30)               
  

• refactor average_biological_replicates_dt and get_additional_variables to support unprettified identifiers

           Changes in version 2024-07-17 (2024-07-17)               
  

• update define_matrix_grid_positions

           Changes in version 2024-07-12 (2024-07-12)               
  

• move get_combo_col_settings and get_iso_colors to gDRplots package

           Changes in version 2024-07-08 (2024-07-08)               
  

• add residual sum of square and p-value to Metrics assay

           Changes in version 2024-07-03 (2024-07-03)               
  

• add vignette section about prettifying logic

           Changes in version 2024-06-24 (2024-06-24)               
  

• fixed issue in vignette

gdsfmt

                   Changes in version 1.40.2                        

UTILITIES

• add “#define STRICT_R_HEADERS 1” to the C++ header file according to R_r86984

• update the C codes according to ‘R_USE_STRICT_R_HEADERS=true’ & ‘R_CXX_USE_NO_REMAP=true’

GeDi

                    Changes in version 1.2.0                        

• Smaller bug and typo fixes

• Fixed the bug that the getGenes() function would set all gene names to all caps which lead to the inability to download the correct PPI information for species like mouse. Also renamed the function to prepareGenesetData() to reflect more accurately its behavior.

• Updated the default version used in the getId() and getStringDB() to 12.0, the current version of the String database.

• Fixed the broken zoom feature in the Optional Filtering Step in the Data Input panel. Additionally added a column Description to the table of zoomed gene sets to facilitate interpretation.

• Fixed that the clustering will now be reset whenever a new score is calculated.

• Updated the checkInclusion() function to drastically reduce runtime.

• Fixed the error that the value of alpha would not be properly pass to all the sub function used by the getpMMMatrix() function.

• Replaced all occurrences of PMM with pMM to match the notation of the original publication.

• Replaced the kNN clustering algorithm with PAM (partitioning around mendoids) as this seems to be more suitable for enrichment data represented by distance scores.

• Renamed the goSimilarity() function to goDistance() to better indicated that this is a distance rather than a similarity score. Also scaled all scores to the [0, 1] interval.

• Fixed the normalization function in the getKappaDistanceMatrix() function.

• Changed the implementation of the Louvain clustering algorithm to use a weighted graph now. The graph is weighted by the distance scores between gene sets.

• Added GeneTonicList as a possible input object for GeDi. Now GeDi is directly compatible with GeneTonic.

GeneNetworkBuilder

                   Changes in version 1.47.4                        

• Add nodeData parameter to polishNetwork function.

                   Changes in version 1.47.3                        
  

• Fix the duplicated parameters in polishNetwork function.

                   Changes in version 1.47.2                        
  

• Add cy3Network function.

                   Changes in version 1.47.1                        
  

• Add edge line-width mapping for polishNetwork function.

GeneTonic

                   Changes in version 2.99.0                        

Other notes

• The transition to the functions available in the mosdef Bioconductor is complete, with the original functions now being deprecated. This applies to goseqTable() (now replaced by mosdef::run_goseq()), which has now been made faster and more robust in its functionality and in the ways it can be executed
• The gene plot widgets now also use the gene_plot() function from mosdef, instead of the previous ggplotCounts() function - gene_plot() is more flexible and has more options to control the behavior of the final plot object
• The deseqresult2tbl() and deseqresult2DEgenes() are now replaced by the more flexible mosdef::deresult_to_df()
• The internally defined createLinkENS(), createLinkGeneSymbol(), and createLinkGO() are now replaced by the equivalent functions in mosdef
• The Roxygen-based documentation now supports markdown. No visible changes should appear to the user, as the content should have stayed fairly the same
• Although no visible changes for the end user are expected, the incoming major version bump will reflect the change in the dependency graph, ensuring that this is noticed at least at the version numbering level

GenomeInfoDb

                   Changes in version 1.42.0                        

BUG FIXES

• Use more robust heuristic in internal helper get_current_Ensembl_release().

GenomicAlignments

                   Changes in version 1.42.0                        

• No changes in this version.

GenomicDataCommons

                   Changes in version 1.30.0                        

New features

• gdc_clinical includes clinical data from the cases.follow_ups.other_clinical_attributes entity (@LiNk-NY).

Bug fixes and minor improvements

• Removed legacy function, methods, endpoints, and arguments (@LiNk-NY)
• Use native pipe |> instead of magrittr::%>% (@LiNk-NY)

GenomicFeatures

                   Changes in version 1.58.0                        

NEW FEATURES

• The TxDb class now extends the new OutOfMemoryObject class defined in BiocGenerics (virtual class with no slots).

• Calling saveRDS() on a TxDb object now raises an error with a message that redirects the user to AnnotationDbi::saveDb().

GenomicPlot

                    Changes in version 1.3.4                        

• Modify pseudo count for ratio matrix

                    Changes in version 1.3.3                        
  

• Add gene id to rownames to heatmap

                    Changes in version 1.3.2                        
  

• Fixed a bug in prepare_3parts_genomic_features

• Add messages to each function

                    Changes in version 1.3.1                        
  

• Updated dependency on R >= 4.4.0 and genomation >= 1.36.0

GenomicRanges

                   Changes in version 1.58.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Use hg38 instead of hg19 in vignettes and examples. See commit 57af07f for the details.

BUG FIXES

• The as.data.frame() methods for GenomicRanges and GPos objects now obey the ‘optional’ argument. See https://github.com/Bioconductor/GenomicRanges/issues/86

GEOquery

             Changes in version 2.99.0 (2024-10-01)                 

New Features

• RNAseq data support for GEOquery. Now you can use RNASeq quantification data prepared by NCBI.
• Basic search in GEO database. Now you can search for datasets in GEO database using GEOquery.
• browseGEO() function to open a web browser with a GEO accession.

Breaking changes

• getGEO() now returns a list of SummarizedExperiment objects. This is a breaking change from previous versions of GEOquery. If you are using GEOquery in a script, you will need to update your code to reflect this change.

Bug Fixes or Improvements

Not an exhaustive list, but some highlights:

• Using httr2 instead of curl for better control over HTTP requests.
• Removed dead gunzip code.

gg4way

                    Changes in version 1.3.1                        

• Helper functions to check DGEdata and a visual unit test

ggmanh

                    Changes in version 1.10                         

New Feature

• Added a visualization that is an extension of manhattan plot called binned manhattan plot. Instead of plotting each individual variant, the variants are binned based on position (x-axis) and log10 p-value (y-axis). More information can be found in the vignette.

• Preprocessing function is binned_manhattan_preprocess and plotting function is binned_manhattan_plot.

Internal Changes

• Change the way positions of the variants are calculated. MPdata now saves the unscaled positions and the scaling is done in manhattan_plot function. (this is for the x-axis)

• To get the actual relative positions used in the manhattan plot, use calc_new_pos() on the MPdata object.

• Gap between chromosomes can be rescaled by using chr.gap.scaling= argument inside manhattan_data_preprocess and manhattan_plot functions.

• Now accounts for negative positions.

ggsc

                    Changes in version 1.3.1                        

• add plot_lisa_feature() (2024-09-06, #34, #39)
• add geom_bgpoint() layer (2024-06-18, Tue, #24)

ggtree

                   Changes in version 3.13.2                        

• mv td_filter(), td_unnest() and td_mutate() to ‘ggfun’ package (2024-10-24, Thu)

                   Changes in version 3.13.1                        
  

• layout argument can be a function to re-calculate the coord of nodes (2024-07-27, Sat, #622)
• layout.params = list(as.graph=TRUE) (by default) for converting the tree to a graph tree (igraph object), so that graph layout can be directly applied to visualize a tree
• otherwise, the function can assume the input tree as a phylo or treedata object
• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)
• mv %<+% operator to ‘ggfun’ (2024-05-28, Tue)

ggtreeSpace

                    Changes in version 1.1.1                        

• update geom_treespace() (2024-09-07)

ginmappeR

                    Changes in version 1.0.7                        

ENHANCEMENT

• Manuals’ examples revised to avoid failing R CMD CHECK on macOS platforms.

                    Changes in version 1.0.6                        
  

ENHANCEMENT

• Test suite revised and enhanced to avoid random failing builds.

                    Changes in version 1.0.5                        
  

BUG FIX

• UniProt to KEGG translation tests fixed.

                    Changes in version 1.0.4                        
  

NEW FEATURES

• Added functions that output databases versions being used: getCARDVersion() getNCBIVersion() getUniProtVersion() getKEGGVersion()

ENHANCEMENT

• Mapping progress indicator added.

• Improved CARD download messages.

BUG FIX

• Functions that use UniProt.ws printing empty lines before the result fixed.

                    Changes in version 1.0.3                        
  

BUG FIX

• UniProt tests fixed.

glmGamPoi

              Changes in version 1.17 (2024-05-29)                  

• test_de can now compute the standard error of the log2-fold change (PR#63, thanks @jackkamm)

• predict now considers the ridge_penalty when calculating the standard errors.

• Detect if smart subset of MatrixGenerics’ rowMeans2 and rowSums2 can be used to speed-up pseudobulk calculation.

GloScope

             Changes in version 1.3.1 (2024-08-01)                  

• Fix bug which caused the gloscope_proportion function to not be properly exported.

GNOSIS

             Changes in version 1.99.0 (2023-09-04)                 

• Made the following significant changes o added functionality to select and upload cBioPortal study o deprecated ability to save R script with executed code

• Submitted to Bioconductor

GOSemSim

                   Changes in version 2.31.1                        

• get_rel_df() to access ontology relation data frame required by the Wang method (2024-08-13, Tue)
• a set of ‘OntDb’ methods for accessing sqlite data generated by the ‘obolite’ package (2024-08-13, Tue)
• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)

goseq

                   Changes in version 1.58.0                        

• Role of maintainer taken over by Federico Marini
• Refreshing the codebase
• introducing roxygen-based documentation
• applying styler for consistent spacing
• using Github Actions for CI/CD
• refined import statements

goSorensen

                    Changes in version 1.7.0                        

We add the following function:

• enrichedIn: This function generates a binary matrix in which the rows represent GO terms, and the columns represent lists. The matrix uses the values TRUE or FALSE to indicate whether each GO term is enriched or not for each list.

In addition:

• We have updated the buildEnrichedTable and allBuildEnrichedTable functions. They now uses the outcomes of enrichedIn to build the contingency table. During the conducted tests, the speed of the procedure for generating contingency tables increased by a factor of six compared to the previous version.

Furthermore, we have included the showEnrichedIn argument in these functions. This is a boolean argument. If the argument is TRUE, in addition to the enrichment contingency table, the function saves a matrix in the global environment, which contains the cross table of the enriched and non-enriched GO terms vs the names of the gene lists generated with the enrichedIn function. This matrix is stored under the name of “enrichedIn_” followed by the name of the ontology and the level being analysed. An object will be produced for every scenario if there are several levels and ontologies.

• We add the vignette “irrelevance-threshold_Matrix_Dissimilarities.” This vignette illustrates calculating, visualizing, and interpreting the irrelevance-threshold matrix of dissimilarities D. This matrix provides dissimilarities between pairs of compared lists. These dissimilarities are not only a descriptive measure but also based on the irrelevance threshold determining whether two lists are equivalent. So, this dissimilarity measure between the two lists is directly associated with their declaration of equivalence.

The matrix D can be represented in interpretable statistic graphs such as dendrograms or biplots, which help to visualize the formation of groups containing equivalent lists. Furthermore, interpreting the biplot dimensions gives us the biological functions responsible for the equivalence between lists.

GRaNIE

             Changes in version 1.9.7 (2024-09-25)                  

Bug fixes

• we made a few adjustments for the still experimental GC correction feature in addConnections_TF_peak() that threw errors for some edge cases when percBackground_size = 0

             Changes in version 1.9.6 (2024-09-01)                  
  

New features

• we now support the mm39 mouse assembly. Please let us know if something does not work. We are currently also generating the TFBS resources for mm39, stay tuned. Once done, the links in the vignette will work.

Improvements

• we now require patchwork version 1.2.0 and above, due to an incompatibility reported between ggplot2 3.5 and patchwork versions < 1.2.0. The error that may be thrown in plotDiagnosticPlots_peakGene is this: Error in Ops.data.frame(guide_loc, panel_loc) : ‘==’ only defined for equally-sized data frames

             Changes in version 1.9.5 (2024-09-01)                  
  

Improvements

• single-cell vignette update, made it clearer which settings to change in the GRaNIE workflow for single-cell data
• warning messages now also contain the name of the function they were originally called from

• forcats warning for package versions of 1.0.0 and above fixed

             Changes in version 1.9.4 (2024-08-01)                  
  

• changed default values for gene.types in filterGRNAndConnectGenes() to all and adjusted documentation across functions that have also this argument - by default, there is now no standard filter for the gene type (genes were filtered to only protein-coding genes before using protein_coding). This results in bigger eGRNs and seems more sensible than to automatically filter genes for most use cases.

             Changes in version 1.9.3 (2024-07-16)                  
  

Bug fixes

• fixed a bug that caused the peak-gene diagnostic plots to incorrectly show background signal in plotDiagnosticPlots_peakGene() (upper right plot on page 1). This was caused by not correctly shuffling the RNA cunts data due to a code change that occurred in version 1.7.4. We apologize for the confusion this may have caused.

          Changes in version 1.9.0-1.9.1 (2024-06-03)               
  

• version jump due to new Bioconductor development cycle

Improvements

• update for the single-cell vignette
• we now provide a public download for the HOCOMOCO v12 TF database for both human (hg38) and mouse (mm10) that can be used as input for GRaNIE in the addTFBS() function. We tested this database extensively and use it as default TF database for our GRaNIE networks.

Bug fixes

• explicitly requiring tidyr 1.3.0 or above due to the usage of separate_wider_delim in the code in a recent upgrade
• fixed an accidental reference to AnnotationHub::getAnnotationHub

GSAR

                   Changes in version 1.40.0                        

• New function ADtest is introduced. It implements a nonparametric multivariate test of means based on the HDP ranking of samples in the MST and the Anderson-Darling statistic.

• New function RADtest is introduced. It implements a nonparametric multivariate test of variance based on the radial ranking of samples in the MST and the Anderson-Darling statistic.

• New function CVMtest is introduced. It implements a nonparametric multivariate test of means based on the HDP ranking of samples in the MST and the Cramer-Von Mises statistic.

• New function RCVMtest is introduced. It implements a nonparametric multivariate test of variance based on the radial ranking of samples in the MST and the Cramer-Von Mises statistic.

GSVA

                    Changes in version 2.00                         

USER VISIBLE CHANGES

• Added a missing data policy for the GSVA and the ssGSEA methods by which missing values in the input expression data either propagate throughout calculations (use=”everything”), prompt an error (use=”all.obs”), or are discarded from calculations (use=”na.rm”).

• The readGMT() function now returns also a GeneSetCollection object, and can automatically identify the type of feature/gene identifier used in the GMT file, adding it to the metadata of the return object.

• Mapping between different types of feature/gene identifiers between gene sets and expression data has been improved.

• Added a new default for the kcdf parameter in the GSVA method, kcdf=’auto’, which tries to select the best value for this parameter, according to the input data.

• Added a new sparse regime of the GSVA algorithm, specifically tailored for expression data stored in sparse matrices, such as single-cell data, to address some of the shortcomings of the original (classical) algorithm with this type of data.

• Added two new methods, gsvaRanks() and gsvaScores(), to run the GSVA algorithm in two steps that provide additional flexibility to score gene sets and extract enrichment information.

• Added a new method gsvaEnrichment() to be used after gsvaRanks(), which allows one to extract enrichment information for a particular gene set and sample/column, including the possibility to produce an enrichment plot using base R or ggplot2 graphics.

• Package messages are now displayed using the cli package, changing and removing some of them, as well as adding other ones, to improve the information reported to the user.

BUG FIXES

• Removed API legacy convenience features, which keep causing problems, as per request of CRAN maintainers.

• Fixed some bugs in the shiny app.

gypsum

                    Changes in version 1.2.0                        

• Switch to rappdirs to choose the cache directory. This allows re-use of the cache with the equivalent Python client.

• Improve handling of unexpected errors with non-JSON bodies.

• Added the unlockProject() utility for administrators.

• Renamed defineTextQuery() to gsc() (for “gypsum search clause”) and generalized it to other fields in the SQLite file. Specifically, it now can filter based on the path to the metadata document, the project, asset or version names, the identity of the uploader and the timestamp of the upload.

• Added the translateTextQuery() function to convert a human-friendly search string into a gypsum.search.clause.

• Renamed searchMetadataText() to searchMetadata(), to reflect the more general nature of the search with the new gsc() function. The old name is now soft-deprecated.

• Renamed searchMetadataTextFilter() to searchMetadataFilter(), to reflect the more general nature of the search. The old name is now soft-deprecated. Added arguments to support custom names/aliases for the project, asset, version and path columns. Deprecated the capability for query= to accept character vectors, callers should supply a gypsum.search.clause directly.

HDF5Array

                   Changes in version 1.34.0                        

NEW FEATURES

• Add ‘as.vector’ argument to h5mread().

SIGNIFICANT USER-VISIBLE CHANGES

• Improvements to coercions from CSC_H5SparseMatrixSeed, H5SparseMatrix, TENxMatrix, or H5ADMatrix to SparseArray:
  • should be significantly more efficient, thanks to various tweaks that happened in the SparseArray and Delayed5Array packages;
  • support coercing an object with more than 2^31 nonzero values.

• Coercion from any of the class above to a sparseMatrix derivative now fails early if object to coerce has >= 2^31 nonzero values.

• All *Seed classes in the package now extend the new OutOfMemoryObject class defined in BiocGenerics (virtual class with no slots).

BUG FIXES

• Fix long standing bug in t() methods for CSC_H5SparseMatrixSeed and CSR_H5SparseMatrixSeed objects.

• Replace internal calls to rhdf5::H5Fopen(), rhdf5::H5Dopen(), and rhdf5::H5Gopen(), with calls to new internal helpers .H5Fopen(), .H5Dopen(), and .H5Gopen(), respectively. See commit 31a7e06 for more information.

hermes

                    Changes in version 1.9.1                        

Miscellaneous

• Change maintainer’s email address.

HIBAG

                   Changes in version 1.42.0                        

• the input of hlaUniqueAllele() can be a hlaAttrBagClass object or a hlaAttrBagObj object

• hlaAlleleToVCF() outputs 0 instead of NaN if the location of HLA gene is unknown or unspecified

• update the C codes according to ‘R_USE_STRICT_R_HEADERS=true’ & ‘R_CXX_USE_NO_REMAP=true’

HicAggR

                    Changes in version 1.1.2                        

• minor fix in doc for preparePlotgardener

                    Changes in version 1.1.1                        
  

• HicAggR is now on bioconductor release 3_19
• added a minor fix to ExtractSubmatrix when using GRanges object to extract, retain only GRanges with seqnames that are present in hicList
• added preparePlotgardener function to generate a data.frame that can be directly used in plotgardener’s plotHicTriangle, plotHicRectangle and plotHicSquare directly

HilbertCurve

                   Changes in version 1.99.0                        

• Add a hilbert curve legend showing the orientation of the curve.

ideal

                   Changes in version 1.99.0                        

Other notes

• The transition to the functions available in the mosdef Bioconductor is complete, with the original functions now being deprecated. This applies to goseqTable() (now replaced by mosdef::run_goseq()), which has now been made faster and more robust in its functionality and in the ways it can be executed
• The gene plot widgets now also use the gene_plot() function from mosdef, instead of the previous ggplotCounts() function - gene_plot() is more flexible and has more options to control the behavior of the final plot object
• The deseqresult2tbl() and deseqresult2DEgenes() are now replaced by the more flexible mosdef::deresult_to_df()
• The internally defined createLinkENS(), createLinkGeneSymbol(), and createLinkGO() are now replaced by the equivalent functions in mosdef
• The Roxygen-based documentation now supports markdown. No visible changes should appear to the user, as the content should have stayed fairly the same
• Although no visible changes for the end user are expected, the incoming major version bump will reflect the change in the dependency graph, ensuring that this is noticed at least at the version numbering level

igvShiny

           Changes in version 2024-08-29 (2024-08-29)               

• fix issue with loading bed files when app is run with query strings

           Changes in version 2024-08-25 (2024-08-25)               
  

• switch from Rcurl::url.exists to httr::http_error (Windows compatibility)

• stop using Amazon S3 URLs by default

           Changes in version 2024-08-16 (2024-08-16)               
  

• fix issue with VCF files

           Changes in version 2024-08-10 (2024-08-10)               
  

• fix issue with custom files not working properly

• sync with Bioconductor (3_19 release)

imcRtools

             Changes in version 1.11.4 (2024-10-28)                 

• changed testdetectCommunity function for group_by parameter

             Changes in version 1.11.3 (2024-10-25)                 
  

• fixed testdetectCommunity function

             Changes in version 1.11.2 (2024-10-08)                 
  

• fixed testInteraction and countInteraction tests due to machine precision issues

             Changes in version 1.11.1 (2024-10-03)                 
  

• fixed BiocNeighbors error for DFrame type data

immunoClust

                 Changes in version 1.37.12-14                      

• CHANGES
  • improvements in meta.clustering process

  • minor changes in plot.immunoClust

                  Changes in version 1.37.3-11                      
    

• CHANGES
  • processing time improvements in meta.SON.clustering and meta.SON.normalisation

IRanges

                   Changes in version 2.40.0                        

BUG FIXES

• Make sure that internal helper coerceToCompressedList() always propagates the mcols.

iSEE

                   Changes in version 2.17.4                        

• Add explicitly a “Stop app” button to close the application (should be a means to nicely behave in container-spawned instances). Addresses #630
• Fix text in ‘configure’ vignette. Closes #626
• Copy information from rowRanges to rowData Closes #637
• Require at least one valid value for atomic, groupable and numeric columns. Closes 660
• If heatmap matrix has no finite values, set the color range arbitrarily. Closes #610
• Limit the number of rows in heatmap annotation legends to 10. Closes #591
• Fix license. Closes #661.
• Rename some internal constants.
• Add checkbox to fix aspect ratio to 1. Closes #541.

• Add checkbox to hide violin boundaries. Closes #619.

                   Changes in version 2.17.3                        
  

• Preserve the existing order of rows when receiving a selection in RowDataTable, ColumnDataTable panels.

                   Changes in version 2.17.2                        
  

• Export function .selectInputHidden().

                   Changes in version 2.17.1                        
  

• Fix typo in setMethod(“.getContinuousMetadataChoices”, “RowDotPlot”, …).

iSEEde

                    Changes in version 1.3.1                        

• Version bump to rebuild classes derived from DotPlot.

iSEEfier

                    Changes in version 1.2.0                        

• Adding in a new function iSEEmarker(), more focused on finding marker genes
• A new iSEEinit() version without the DynamicMarkerTable panel
• Expanding the input of iSEEinit() to accept features as data.frame in addition to vector
• Adding visualization plots to iSEEnrich()

iSEEhex

                    Changes in version 1.7.1                        

• Version bump to rebuild classes derived from DotPlot.

iSEEhub

                    Changes in version 1.7.1                        

• Version bump to rebuild classes derived from DotPlot.

iSEEindex

                    Changes in version 1.3.2                        

• Added a full implementation of the runr resource class, defining its behavior with simple heuristics based on the fact that users can now also provide not just a path but the call to the command of R to be run (therefore, the name runr) to obtain an object to explore. A typical use case would be to deploy a collection of datasets from a data package.

                    Changes in version 1.3.1                        
  

• Version bump to rebuild classes derived from DotPlot.

iSEEpathways

                    Changes in version 1.3.1                        

• Version bump to rebuild classes derived from DotPlot.

iSEEu

                   Changes in version 1.17.1                        

• Version bump to rebuild classes derived from DotPlot.

IsoBayes

                    Changes in version 1.2.5                        

• inference function extended (map_iso_gene can be either be a data.frame or a .csv)

                    Changes in version 1.2.3                        
  

• plot_traceplot added

                    Changes in version 1.2.2                        
  

• bug in “input_data” fixed (only triggered when using PEP with MM data)

                    Changes in version 1.2.1                        
  

• normalization constant added (accounting for N detected peptides)

isomiRs

                   Changes in version 1.33.1                        

• fix isoAnnotate error due to duplicates lines https://github.com/lpantano/isomiRs/issues/18

KEGGREST

                   Changes in version 1.46.0                        

BUG FIXES

• 1.45.1 Fix keggFind URL to use ‘+’ instead of spaces.

lefser

                   Changes in version 1.15.10                       

• [Major] Name of the two arguments for lefser function is changed from groupCol and blockCol to classCol and subclassCol, respectively.
• [Major] Defunct expr argument in lefser
• [New function] lefserPlotFeat plots the histogram of relative abundance (in the (0,1) interval) of the selected features
• [New function] lefserPlotClad draws the cladogram of the significantly more abundant taxa and their LDA scores
• [New function] lefserClades runs the lefser, returning additional information (e.g., agglomerates the features abundance at different taxonomic ranks) required for lefserPlotClad.

• [New feature] Visualization functions are using a color-blind friendly color palette by default.

                   Changes in version 1.15.7                        
  

• [Major algorithm update] We remove the step (createUniqueValues) in the lefser function, which used to add small random numbers to make all the values unique. Potential issues (e.g., LDA) due to excess 0s should be managed by filtering out low abundant features from the input.

                   Changes in version 1.15.3                        
  

• The column names of lefser output is changed to c(“features”, “scores”) from c(“Names”, “scores”)
• [New feature] The get_terminal_nodes function to select only the terminal nodes of the hierarchical features (e.g., taxonomic data).
• [Major algorithm update] Add an option for adjusting the first Kruskal-Wallis Rank Sum Test and Wilcoxon-Rank Sum test for multiple hypothesis testing through the new argument method in the lefser function.

lemur

                     Changes in version 1.3                         

• lemur now automatically inserts the variables from the design formula into the group_by argument for find_de_neighborhoods. (thanks Katha for pushing for this feature)
• The formula parsing automatically detects global variables and adds them to the colData. This avoids problems with the random test / training assignment.
• Duplicate column names in colData are now longer allowed.
• Require harmony version >= 1.2.0 (thanks Maija for reporting the problem)

limma

                   Changes in version 3.62.0                        

• New function fitFDistUnequalDF1() for improved empirical Bayes hyperparameter estimation. The new function is an alternative to the long-standing limma functions fitFDist() and fitFDistRobustly(). The new function gives special attention to contexts where the df1 argument is unequal between cases or can include small fractional values, such as those resulting from edgeR’s voomLmFit() or from the edgeR 4.0 quasi-likelihood pipeline. The new function uses profile maximum likelihood instead of moment estimation to estimate df.prior, and so may be more accurate than fitFDist() or fitFDistRobustly() even when the df1 values are all equal. The new hyperpameter estimation will be used by default by eBayes(), treat() and squeezeVar() whenever the residual degrees of freedom are unequal, but users can request legacy behavior for those functions by setting legacy=TRUE.

• New argument adaptive.span for voomWithQualityWeights() and normalizeCyclicLoess(), with the same purpose as the same argument for voom(). If TRUE then an optimal value for the span is chosen based on the number of genes in the dataset. voom() and voomWithQualityWeights() now return the chosen span as part of the output object if adaptive.span=TRUE.

• contrasts.fit() now converts the coefficient name “(Intercept)” created automatically by model.matrix() to “Intercept”, same as is done by makeContrasts(). This should avoid inconsistent coefficient names between the fitted model object and contrast matrices created by makeContrasts().

• New argument keep.EList for voomaLmFit(), similar to the same argument for edgeR::voomLmFit(). The observation weights generated by voomaLmFit() are now stored only if keep.EList=TRUE.

• voomaByGroup() now uses the overall mean-variance trend for groups with only one sample, for which a separate trend is not estimable.

• Add Ravindra et al (2023) as a reference and Mengbo Li as an author to the voomaByGroup() help page. Emphasize in the help details that only simple design matrices are supported by this function.

• Revise the eBayes/treat help page to further clarify the legacy and fc arguments.

• Bug fix to voomaByGroup() to save variance plot parameters correctly when save.plot=TRUE.

• Remove argument zero.weights from the MArrayLM method for plotMD() and plotMA().

• Fix bug in the MArrayLM methods for plotMD() and plotMA(), which were attempting to access a weights component of the fitted model object, analogously to what plotMD() does with the EList or MAList objects, even though MArrayLM objects do not contain a weights component.

• Use of the stats package digamma() function replaced with statmod’s logmdigamma() in fitFDist(), fitFDistUnequalDF1() and intraspotCorrelation(). Slight improvements to speed, accuracy and code simplicity, but results should remain the same to at least 13 significant figures.

Macarron

                    Changes in version 1.9.1                        

• Synced Version with Bioconductor

• Added citation

• Updated README

• Changed heatmap plotting default to FALSE

• Corrected curly bracket placement in wrapper

MACSr

                   Changes in version 1.13.1                        

• Upgrade to MACS 3.0.2.

maftools

                   Changes in version 2.22.0                        

BUG FIXES

• Bug fix in using keepGeneOrder in coOncoplot(). Issue: 1061
• Bug fix in using selectedPathways in oncoplot(). Issue: 1041
• Add an error message when bai files are missing sampleSwaps(). Issue: 1028
• Bug fix in tmb while handling multiple MAFs. Issue: 1018
• Handle missing NAs while sub-setting for ranges. Issue: 1013
• Better error handling when zero mutated samples are encountered in clinicalEnrichment. Issue: 1010
• MAJOR: read.maf by default coerces clinical data columns to character. This bug fix avoids it and is auto detected. Issue: 997

ENHANCEMENTS

• Better handling of color codes for continuous variable annotations 1053
• Add right_mar to gisticOncoPlot1043
• Added PPDPFL to protein domain database Issue: 1025
• Better sorting of oncoplot with collapsePathway
• Changed default background for oncoplot from gray to #ecf0f1
• Changed default signature database to SBS_v3.4 (from legacy)
• Update tmb function

BREAKING CHNAGES

• Column order required for pathways() function changed from Pathway,Gene to Gene,Pathway. Issue: 1041

NEW FUNCTIONS

• gisticCompare() for comparing two GISTIC objects
• segSummarize() for summarizing DNAcopy segments

MatrixQCvis

             Changes in version 1.13.5 (2024-06-27)                 

• add log10 as transformation method in transformAssay

• add “none” as imputation method in imputeAssay

• update shiny application with log10

• update vignette with log10

• update unit tests with log10 and “none”

             Changes in version 1.13.4 (2024-06-24)                 
  

• update vignette, add information on ComBat

             Changes in version 1.13.3 (2024-06-21)                 
  

• add functionality to perform batch correction using sva::ComBat

• improve visualisation of MAplot in shinyQC

             Changes in version 1.13.2 (2024-06-11)                 
  

• use DT::renderDT instead of shiny::renderDataTable

• use DT::DTOutput instead of shiny::dataTableOutput

             Changes in version 1.13.1 (2024-04-25)                 
  

• add batch2 and … arguments in batchCorrectionAssay

matter

             Changes in version 2.7.10 (2024-10-16)                 

NEW FEATURES

• Add ‘fetch’ and ‘flash()’ for base R types

SIGNIFICANT USER-VISIBLE CHANGES

• Update ‘fetch()’ and ‘flash()’ to pass more arguments to underlying ‘matter’ constructors

                    Changes in version 2.7.9                        
  

NEW FEATURES

• Add ‘pivots’ argument to ‘fastmap()’ to support more than 2 pivot candidates per iteration

SIGNIFICANT USER-VISIBLE CHANGES

• Update ‘fetch()’ and ‘flash()’ to preserve atoms types

• Update ‘fetch()’ and ‘flash()’ to fall back to serial execution if BPPARAM is a distributed cluster

BUG FIXES

• Add ‘chunkopts’ to ‘nscentroids()’ and ‘sgmix()’ signatures to fix downstream ‘…’ bugs

• Fix graphical parameters not applying to vizi plots

                    Changes in version 2.7.8                        
  

BUG FIXES

• Fix shared memory segmentation faults on Linux

• Fix voxel plotting when length(unique(z)) == 1L

                    Changes in version 2.7.7                        
  

NEW FEATURES

• New ‘fetch()’ and ‘flash()’ generics for moving data between file storage and shared memory

SIGNIFICANT USER-VISIBLE CHANGES

• Support both number of items OR size in bytes when setting getOption(“matter.default.chunksize”)

• Now using ‘@’ prefix as shared memory identifier for file system compatibility (e.g., Windows)

• Deprecated ‘sgmixn()’; updated ‘sgmix()’ to support multichannel images directly

• Improved RNG behavior for non-L’Ecuyer seeds

BUG FIXES

• Fix potential infinite loop in ‘mi_learn()’

• Add warning in chunk-apply functions if ‘RNG=TRUE’ but ‘RNGkind()’ is not “L’Ecuyer-CMRG”

                    Changes in version 2.7.6                        
  

SIGNIFICANT USER-VISIBLE CHANGES

• Add ‘cpals()’ and ‘dpals()’ to list available palettes

• Moving ‘simple_logger’ now appends ‘sessionInfo()’

• Statistical methods ‘fastmap()’ and ‘nscentroids()’ now use ‘rowDists()’ and ‘colDists()’ directly

• Optional argument ‘distfun’ has new requirements in methods ‘fastmap()’ and ‘nscentroids()’

• Class ‘matter_str’ now inherits from ‘matter_list’ for consistency between R and C++ interfaces

• Export ‘.rowDists()’ and ‘.colDists()’ functions

BUG FIXES

• Fix ‘simple_logger’ finalizer on R session exit

                    Changes in version 2.7.5                        
  

NEW FEATURES

• Shared memory support comes to ‘matter’ via boost!

• Add ‘as.shared()’ for coercion to shared memory ‘matter’ objects

• Use ‘path=”:memory:”’ to construct ‘matter’ object in shared memory

• Use ‘mem()’ to monitor shared memory usage

SIGNIFICANT USER-VISIBLE CHANGES

• Add shared memory support to ‘mem()’ output

• Add cluster memory support to ‘memtime()’ output

• Add cluster memory monitoring with ‘memcl()’ function

• New documentation for several previously-undocumented utility functions that may be useful for others

• New ‘permute’ argument in chunk-apply functions

BUG FIXES

• Improved behavior for the general ‘matter()’ constructor

• Use private RNG for ‘uuid()’ to avoid collisions from ‘set.seed()’ and to avoid changing ‘.Random.seed’

• Fix ‘is_gridded()’ and ‘to_raster()’ behavior for non-integer coordinates and character rasters

                    Changes in version 2.7.4                        
  

NEW FEATURES

• Add ‘SnowfastParam’ class to support PSOCK clusters for faster startups and faster serialization

• Add getOption(“matter.default.chunksize”) for setting the approximate size of chunks in bytes

• Add getOption(“matter.default.serialize”) for managing serialization behavior in chunk-apply functions

• New ‘simple_logger’ class for writing log files

• New ‘options(matter.temp.dir=tempdir())’ replaces the previous ‘options(matter.dump.dir=tempdir())’

• New ‘options(matter.temp.gc=TRUE)’ controls whether temporary matter files are automatically removed when all R objects referencing them are garbage collected

• Temporary matter files are now garbage collected!

SIGNIFICANT USER-VISIBLE CHANGES

• New ‘chunkopts’ argument replaces ‘nchunks’ and includes the new chunk options (“chunksize” and “serialize”)

BUG FIXES

• Fix leaky closures in internal chunk loop functions causing slow parallel performance on large datasets

• Fix internal bug in ‘eval_exprs()’ where ‘recursive’ attribute was always set to ‘TRUE’

                    Changes in version 2.7.3                        
  

NEW FEATURES

• Add new functions ‘knnmax()’ and ‘knnmin()’

• Add new functions ‘filtn_ma()’, ‘filtn_conv()’, etc.

• Add support for N-dimensional signals to ‘estnoise_*()’ functions

• Add ‘findpeaks_knn()’ for KNN-based peak detection

SIGNIFICANT USER-VISIBLE CHANGES

• Add signal processing vignette

• Faster ‘knnsearch()’ when the data and query are the same

• Ties in ‘knnsearch()’ are now broken based on data order

• Updated ‘estnoise_sd()’, ‘estnoise_mad()’, and ‘estnoise_quant()’

BUG FIXES

• Improvements to ‘filt1_adapt()’ and ‘filt2_adapt()’

                    Changes in version 2.7.2                        
  

NEW FEATURES

• Support 2D signals in ‘plot_signal()’ (e.g., for ion mobility)

• New argument ‘alphapow’ in ‘plot_signal()’ and ‘plot_image()’

SIGNIFICANT USER-VISIBLE CHANGES

• Plot method for ‘vizi_bars’ now sums duplicate bar counts

BUG FIXES

• Fix chunk-apply functions for BPPARAM=NULL

• Fix ‘chunkMapply()’ named list errors

• Fix ‘is_gridded()’ so infinite ‘estres()’ result gives FALSE

• Give more useful error messages for ‘dpal()’ and ‘cpal()’

• Fix alpha channel in ‘plot_image()’

                    Changes in version 2.7.1                        
  

NEW FEATURES

• Support subsetting of deferred operations

• Add ‘chunked’ classes for chunked objects

• Add ‘s_stat()’ for grouped streaming statistics

• For ‘plot_image()’, set ‘useRaster’ to plot 3d surface/volume vs voxels

• Add ‘enhance_adj()’ function for adjusting extreme values

SIGNIFICANT USER-VISIBLE CHANGES

• Performance improvements for chunk-apply functions

• Support chunk-apply functions on remote cluster workers

• Reduced memory usage for chunk-apply functions on SNOW clusters

• Image smoothing ‘filt2_*()’ functions support multiple channels

• Contrast enhancement ‘enhance_*()’ functions support multiple channels

• Remove ‘biglm’ from imports

BUG FIXES

• Fix subplot axis scaling and aspect ratio for ‘plotly’ graphics

• Fix passing colors to line charts for ‘plotly’ graphics

                    Changes in version 2.6.3                        
  

BUG FIXES

• Fix ‘filt2_gauss()’ behavior with NAs

                    Changes in version 2.6.2                        
  

BUG FIXES

• Fix ‘sgmixn()’ on ‘matter_mat’ and ‘sparse_mat’ input

                    Changes in version 2.6.1                        
  

BUG FIXES

• Fix ‘matter_list’ error on zero-length elements

memes

                   Changes in version 1.13.1                        

• Fixed an error in importAme that prevented import when runAme was run with sequences = TRUE (Reported by @withermatt on Github. Thank you!)

meshes

                   Changes in version 1.31.1                        

• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)

metabCombiner

                   Changes in version 1.15.2                        

• Bug fixes for duplicate column names

                   Changes in version 1.15.1                        
  

• New m/z shift modeling functionality added:
  • mzFit(): m/z shift modeling and plotting function
  • mzfitParam(): parameter list function for listing modeling parameters
• update to calcScores():
  • new arguments (mzshift and mzfit) for m/z correction before scoring
• new citation

MetaboAnnotation

                     Changes in version 1.9                         

Changes in 1.9.2

• Fix missing ProtGenerics dependency.

Changes in 1.9.1

• Add parameter scalePeaks to plotSpectraMirror to allow scaling peak intensities before plotting.

metabolomicsWorkbenchR

                   Changes in version 1.15.1                        

• fix untarg import

methyLImp2

             Changes in version 1.1.1 (2024-09-10)                  

• Fixing wrong error/warning messages;

• Adding example of user-provided annotation.

             Changes in version 1.0.1 (2024-07-03)                  
  

• Fixing warnings printing.

mia

                    Changes in version 1.13                         

• Added new functions getMediation and addMediation

• replace getExperiment* and testExperiment* functions with getCrossAssociation

• Replace mergeRows and mergeCols with new function agglomerateByVariable

• agglomerateByRank: bugfix related to agglomeration of non-existing tree

• getHierarchyTree: bugfix related to empty cells in rowData

• agglomerateByRank: bugfix: trees was not pruned correctly

• rename meltAssay to meltSE

• Rename countDominantFeatures and countDominantTaxa to summarizeDominance

• rename subsetByPrevalent* and subsetByRare* to subsetByPrevalent and subsetByRare

• Deprecate transformFeatures, transformSamples, transformCounts, Ztransform, relAbundanceCounts

• rename getRare* functions to getRare, getUnique* functions to getUnique, getTop* functions to getTop and getPrevalent* functions to getPrevalent

• Rename subsampleCounts to rarefyAssay

• Rename perSampleDominant* functions to getDominant and addPerSampleDominant* functions to addDominant

• Rename splitByRanks to agglomerateByRanks and add option as.list

• Explain that rarefyAssay returns a new SummarizedExperiment object that includes the newly added subsampled assay.

• Fix bug in mergeFeaturesByPrevalence

• new aliases calculateDPCoA to getDPCoA, calculateNMDS to getNMDS, calculateRDA to getRDA, calculateCCA to getCCA

• add informative error message in rarefyAssay on assays with strictly-negative values

• Use rbiom package in unifrac implementation

• Updated parameter names to follow naming convention “parameter.name”

• rename converters makeTreeSEFrom* to convertFrom* and makePhyloseqFromTreeSE to convertToPhyloseq

• add rowTree agglomeration and RefSeq agglomeration in agglomerateByPrevalence

• Fix tree merging in unsplit and mergeSEs functions

• Added addAlpha; a wrapper for calculating all alpha diversity indices

• Added importTaxpasta

• Changes in default taxonomy ranks; more ranks supported

• Added Tito2024QMP dataset

• Added convertToBIOM

• new methods getLDA and addLDA for LDA ordination with feature loadings computation

• new methods getNMF and addNMF for NMF ordination with feature loadings computation

• If missing values, give informative error in RDA/CCA functions

• transformAssay can apply transformation to altExp

• Added CSS transformation

• In agglomerateByVariable, splitOn and getDominant, use ‘group’ to specify grouping variable.

miaViz

                    Changes in version 1.13                         

• plot*Tree: bugfix, ununique nodes

• Added confidence.level parameter to plotCCA

• add plotNMDS to miaViz (plotNMDS deprecated in mia)

• Added getNeatOrder function

• plotAbundance: enable plotting without agglomeration

• Change parameter naming convention from parameter_name to parameter.name

• Added plotLoadings function

MicrobiomeProfiler

                   Changes in version 1.11.1                        

• support gson for PubChem Pathway (2024-08-16, Fri, #6)

MicrobiotaProcess

                   Changes in version 1.17.1                        

• update scale_fill_diff_cladogram to be compatible with ggnewscale

  = 0.5.0 (2024-07-24, Wed)

                   Changes in version 1.17.0                        
  

• Bioconductor 3.19 release, and Biocondutor 3.20 (devel) version bump. (2024-05-14, Tue)

miloR

             Changes in version 2.0.1 (2024-04-30)                  

• Introduce NB-GLMM into Milo 2.0 for random effect variables and modelling dependencies between observations
• Diagnostic function for checking model separation for experimental variables, i.e. splitting zero from non-zero counts perfectly
• Vignette describing basic usage of GLMM functions in testNhoods

MIRit

                    Changes in version 1.1.1                        

Changes were made to ensure that R CMD check runs without errors or warnings. Moreover, MIRit has been updated to use the new miRTarBase version 10 database.

miRSM

                    Changes in version 2.1.2                        

• Update CITATION <2024-09-18, Wed>

                    Changes in version 2.1.1                        
  

• Update module_FA function <2024-08-25, Sun>

miRspongeR

                    Changes in version 2.9.1                        

• Update moduleDEA function <2024-08-25, Sun>.

monaLisa

                   Changes in version 1.11.3                        

• add show_bin_legend argument to plotMotifHeatmaps (contributed by @danymukesha, PR #62)

MOSClip

                    Changes in version 1.0.0                        

• Initial BioConductor submission.
• New topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated gene modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.

mosdef

                    Changes in version 1.2.0                        

• New functionality added for general scope tasks, such as feature annotation and summaries on the expression tables
• The gene_plot() function now is (again) able to handle the specification of more than one grouping variable

MOSim

             Changes in version 2.1.0 (2024-05-09)                  

• Added TF simulation to scMOSim

motifStack

                   Changes in version 1.49.1                        

• Fix the issue for importMatrix when ‘w’ is missing.

motifTestR

                    Changes in version 1.1.5                        

• Added clusterMotifs, testClusterPos and testClusterEnrich
• Enforced strict use of PWMs for all functions

MouseFM

             Changes in version 1.14.1 (2024-08-26)                 

• Backend server changed

mpra

                   Changes in version 1.27.2                        

• Add endomorphic option to return MPRASet as a final result

• Add library size default option for normalization

                   Changes in version 1.26.1                        
  

• Pass in block vector in normalize_counts() call in .fit() functions

msa

                   Changes in version 1.37.4                        

• change of interface of msaPrettyPrint() function in order to allow for a workaround for texi2dvi() problems (using quiet=TRUE and index=FALSE together throws an error)

                   Changes in version 1.37.3                        
  

• fix of major bug in the Muscle interface

                   Changes in version 1.37.2                        
  

• further fix of ClustalOmega makefile and source code to ensure compatibility with new Rcpp version (further adaptations for MacOS platform)

                   Changes in version 1.37.1                        
  

• fix of ClustalOmega makefile and source code to ensure compatibility with new Rcpp version

MsBackendMassbank

                    Changes in version 1.13                         

Changes in 1.13.1

• Add extractByIndex() method.

MsBackendMetaboLights

                    Changes in version 0.99                         

Changes in 0.99.1

• Add mtbls_sync() to synchronize a MsBackendMetaboLights object.
• Add mtbls_sync_data_files() function to cache selected files and mtbls_cached_data_files() to list all locally cached data files.

Changes in 0.99.0

• Prepare package for submission to Bioconductor.

MsBackendSql

                     Changes in version 1.5                         

Changes in 1.5.1

• Implement the new extractByIndex() methods.

MsCoreUtils

                    Changes in version 1.17                         

MsCoreUtils 1.17.3

• Use R_Calloc and R_Free instead of Calloc and Free in src/lowerConvexHull.c, respectively, to reflect changes in the R API and fullfil STRICT_R_HEADERS check.

MsCoreUtils 1.17.2

• Fix typo in normalisation methods description.

MsCoreUtils 1.17.1

• Fix common_path() to not return also the file name if the input parameter contains only identical character strings.

MSnbase

                    Changes in version 2.31                         

MSnbase 2.31.2

• Suggest pRolocdata (>= 1.43.2.1) (that has some extdata, needed to other packages’ vignettes).

MSnbase 2.31.1

• Disable nested parallel processing for chromatogram() method.

• Fix Rd notes.

                   Changes in version 2.31.0                        
  

• New Bioconductor devel.

msPurity

                   Changes in version 1.30.1                        

• Update example for purityX causing build error

MSstatsConvert

                   Changes in version 1.16.0                        

• Improved memory management for efficiency.
• Added support for ProteinProspector data conversion to MSstatsTMT format.
• Updated NA handling for Skyline and Spectronaut converters
• Added MetaMorpheus converter functionality.

MultiAssayExperiment

                   Changes in version 1.32.0                        

Bug fixes and minor improvements

• Various documentation improvements to MultiAssayExperimenToMAF, saveHDF5MultiAssayExperiment, and reexports

• When rownames are numeric characters e.g., “1”, ensure they stay character when converting MultiAssayExperiment to longFormat.

                   Changes in version 1.30.2                        
  

Bug fixes and minor improvements

• The colData<- replacement method now correctly works with data.frame value inputs (@drighelli, #330).
• Updated CITATION information in the main vignette.
• Use reshape2::melt instead of stats::reshape to preserve row names in longFormat

multiGSEA

             Changes in version 1.15.1 (2024-10-22)                 

• Remove proteomics feature with empty identifier to prevent errors in vignette building.

MungeSumstats

                   Changes in version 1.13.7                        

Bug fix

• infer_eff_direction now includes A0 as an ambiguous case as well as A1/A2.

New features

• eff_on_minor_alleles parameter added (off by default) - controls whether MungeSumstats should assume that the effects are majoritively measured on the minor alleles. Default is FALSE as this is an assumption that won’t be appropriate in all cases. However, the benefit is that if we know the majority of SNPs have their effects based on the minor alleles, we can catch cases where the allele columns have been mislabelled.

                   Changes in version 1.13.6                        
  

New features

• Mappings added to mapping file for risk and non risk allele.

                   Changes in version 1.13.3                        
  

Bug fix

• Bug fix for check 3 in infer effect column - previously A1 & A2 were swapped when there were more matches for the ref genome in A1 rather than A2 which was incorrect. Corrected now so it will only be flipped when A2 has more matches to the reference genome.

                   Changes in version 1.13.2                        
  

New features

• Handling of -log10 p-values (outside of VCFs) added.

                   Changes in version 1.13.1                        
  

New features

• Mapping for OA (other Alllele) added to A1.

muscat

                   Changes in version 1.19.1                        

• added J Gilis, D Risso, L Clement as authors

• differential detection with ‘pbDS(…, method=”DD”)’ or ‘pbDD()’ & stagewise testing [Gilis et al.], plus corresponding vignette

• replace ‘aes_string()’ in ‘ggplot()’ by ‘.data$.’ from ‘rlang’

musicatk

             Changes in version 1.14.1 (2024-07-13)                 

• Removed deconstructSigs

mzR

                   Changes in version 2.39.2                        

• Improve openMSfile and openIDfile manual page (contirbuted by rdhale92, PR #299)

                   Changes in version 2.39.1                        
  

• Update CV translator, adds support for Astral

NanoMethViz

                    Changes in version 3.1.0                        

• Fixed parsing error for BAM files leading to an extre site to be called whenever skip width is greater than 0.
• Added functions get_cgi_*() to get CpG islands annotation for mm10, GRCm39, hg19, and hg38.
• Changed colour palette for heatmaps to have a less bright yellow on the low end.
• Changed default NanoMethViz.site_filter value to 3. This filters out any sites with less than 3 coverage.
• Changed BAM file parsing behaviour when parse flag “.” or “?” is not set to default to “?”. This is against SAM spec but follows the behaviour of IGV and older PacBio datasets.

nipalsMCIA

             Changes in version 1.2.1 (2024-08-31)                  

Major changes

Minor improvements and bugfixes

• Updated ‘Single-Cell-Analysis’ vignette to remove potential issue with BiocFileCache having two copies of data.
• Updated author list and citation.
• Updated references in readme.

NormalyzerDE

                   Changes in version 1.23.2                        

• Fix bug where non-categorical ANOVA setting wasn’t applied

                   Changes in version 1.23.1                        
  

• Remove unnecessary dependency (Biobase) by calling rowMedians with matrixStats::rowMedians instead

• Fix deprecation warning by using guide = “none” instead of FALSE

omicsViewer

                    Changes in version 1.10                         

new features

• dynamic heatmap - zoomed in heatmap upon subsetting features and observations

ompBAM

             Changes in version 1.9.1 (2024-07-27)                  

• Remove dependency on zlibbioc

OncoSimulR

             Changes in version 4.7.8 (2024-10-09)                  

• Remove support for maOS with arm64 (i.e., kjohnson3 and kjohnson1 machines).

             Changes in version 4.7.7 (2024-09-18)                  
  

• Try to work around (and ask for help) for tests that fail in the BioC kjohnson3 machine (maOS 13.6.5, arm64). Yes, more of this.

             Changes in version 4.7.6 (2024-09-16)                  
  

• Try to work around (and ask for help) for tests that fail in the BioC kjohnson3 machine (maOS 13.6.5, arm64). Yes, more of this.

             Changes in version 4.7.5 (2024-09-12)                  
  

• Try to work around (and ask for help) for tests that fail in the BioC kjohnson3 machine (maOS 13.6.5, arm64).

             Changes in version 4.7.4 (2024-07-30)                  
  

• Try to work around (and ask for help) for a vignette example that fails in the BioC kjohnson3 machine (maOS 13.6.5, arm64). (Yes, a fourth place where it fails).

             Changes in version 4.7.3 (2024-07-26)                  
  

• Try to work around (and ask for help) for a vignette example that fails in the BioC kjohnson3 machine (maOS 13.6.5, arm64). (Yes, a third place where it fails).

             Changes in version 4.7.2 (2024-07-25)                  
  

• Try to work around (and ask for help) for a vignette example that fails in the BioC kjohnson3 machine (maOS 13.6.5, arm64). (Yes, a second place where it fails).

             Changes in version 4.7.1 (2024-07-23)                  
  

• Try to work around (and ask for help) for a vignette example that fails in the BioC kjohnson3 machine (maOS 13.6.5, arm64).

• Miscell minor: incorporate 361ccdc to 1bc3cbd (in main github repo) to the BioC version.

• Fixed Note “Lost braces in \itemize; meant \describe ?”

• Updated vignette address to IIBM new name.

ontoProc

                   Changes in version 1.99.4                        

• caching the RDS version of ontology_index so setup_entities2() is fast after first call

• exploring role for bioregistry from pypi – added a bioregistry_ols_resources function

                   Changes in version 1.27.1                        
  

• added search_labels(), to use owlready2 search facility on term labels

orthos

                    Changes in version 1.3.1                        

• Environment installation addresses Anaconda licencing changes

                    Changes in version 1.3.0                        
  

• Bioconductor Release update

pathlinkR

                   Changes in version 1.1.22                        

• Expanded and clarified error messages for pathwayEnrichment input

• Updated vignette

                   Changes in version 1.1.18                        
  

• Fixed bug for pathwayEnrichment when running fgsea (NA gene names)

                   Changes in version 1.1.17                        
  

• Fix for default parameters and theme settings in ppiPlotNetwork
• Support for GSEA (via package fgsea), both as an option in pathwayPlots and pathwayEnrichment

• Global fontSize argument added to pathwayPlots

                   Changes in version 1.1.10                        
  

• Support for KEGG pathways when running pathwayEnrichment, either through Sigora or traditional over-representation

                    Changes in version 1.1.8                        
  

• pathwayPlots now supports the output from fgsea on Reactome pathways (109a173)

                    Changes in version 1.1.7                        
  

• Size of asterisks in pathwayPlots is set based on tringle size (1f9b751)

                    Changes in version 1.1.6                        
  

• Updated installation information in README
• “eruption” gained argument “labelCutoffs” to add labels to p value and fold change cutoff lines
• “ppiPlotNetwork” checks for argument “labelColumn” when “label=TRUE”
• Fixed some tests

pcaExplorer

                   Changes in version 2.99.0                        

New features

• The pcaplot() function now provides a clever default for the intgroup parameter, if some content (as it should) is provided in the colData slot of the main input object

Other notes

• The transition to the functions available in the mosdef Bioconductor is complete, with the original functions now being deprecated. This applies to topGOtable() (now replaced by mosdef::run_topGO())
• The gene plot widgets now also use the gene_plot() function from mosdef, instead of the previous undocumented internal function
• The Roxygen-based documentation now supports markdown. No visible changes should appear to the user, as the content should have stayed fairly the same
• Although no visible changes for the end user are expected, the incoming major version bump will reflect the change in the dependency graph, ensuring that this is noticed at least at the version numbering level

Pedixplorer

                    Changes in version 1.1.5                        

• Change code of ped_to_legdf
• When plotting with the main plot, the legend gets its own space separate from the plot. This allow better control over the size and localisation of the legend.
• The graphical parameters are reset after each use of plot_fromdf
• Add tooltips control in Pedigree plots and add it to the app
• Add example of interactivness in vignette

• Fix plot area function and legend creation for better alignment

                    Changes in version 1.1.4                        
  

• Update website and logo
• Improve ped_shiny() esthetics
• Change plot element order rendering for better looks
• Add more control to line width of box and lines
• Improve legend ordering
• Separate website building workflow from check
• Update function documentation and set to internal all unnecessary functions for users
• Stabilize unit test
• Standardize the vignettes and add more documentation

• Fix label adjusting position in plot functions

                    Changes in version 1.1.3                        
  

• Fix github workflows
• Disable ped_shiny() execution in markdown

• Publish with pkgdown

                    Changes in version 1.1.2                        
  

• Use R version 4.4 and update workflows

                    Changes in version 1.1.1                        
  

• A shiny application is now available through the ped_shiny() function.
• Function imports have been cleaned.
• Unit tests have been added as well as more snapshot to increase package coverage.
• relped dataset allows to easily test special relationship.
• Documentation is enhanced and correctly linted.
• precision parameter has been added to align4() and set_plot_area() to reduce noise between platform.
• fix_parents() has been fixed and improved.
• More controls over color setting with generate_colors().
• Possibility to force computation of alignement when it fails with force = TRUE.
• upd_famid_id() to upd_famid().
• Zooming in a pedigree object is now done by subsetting the dataframe computed by ped_to_plotdf().
• useful_inds() function has been improved.

pgxRpi

             Changes in version 1.1.8 (2024-10-11)                  

• Added support for accessing and visualizing level-specific CNV frequency data.

• Enabled calculation of level-specific CNV frequencies from segment data.

             Changes in version 1.1.7 (2024-09-11)                  
  

• Adapted to Progenetix API change: updated endpoint from “analyses/?output=cnvstats” to “services/cnvstats/”.
• The dataset parameter in pgxLoader is now used to select datasets directly from the Beacon response, rather than being used internally.

• Modified pgxSegprocess to support usage with downloaded “pgxseg” files from Progenetix.

             Changes in version 1.1.6 (2024-08-05)                  
  

• Modified extract_general_results function to ensure it adapts correctly to arrays.
• Moved callset and cnvstats data from the “g_variant” type to “cnv_fraction” to better align with data types.

• Removed the pgxCount function and integrated its functionality into pgxLoader with the “sample_count” type, streamlining such query.

             Changes in version 1.1.5 (2024-07-30)                  
  

• Added config/datatable_mappings.yaml to define mapping rules between Beacon JSON responses and data tables.
• Modified metadata access to retrieve data directly from the Beacon API instead of using the services/sampletable API.
• Enabled querying of analyses information.
• Updated the type parameter in pgxLoader to align more closely with Beacon v2 model entities: biosamples, individuals, analyses, and g_variants.
• Added entry_point parameter to pgxLoader.
• Removed filterLogic parameter from pgxLoader.
• Optimized parallel query for variants.

• Cleaned up code and vignettes.

             Changes in version 1.1.3 (2024-06-14)                  
  

• Add pgxMetaplot function to generate survival plots from metadata

• Add num_cores parameter for parallel query of variants

             Changes in version 1.1.2 (2024-05-03)                  
  

• Add segtoFreq function to allow CNV frequency calculation from given segment data

phantasus

                   Changes in version 1.25.5                        

• reworked annotation parsing

phenomis

                    Changes in version 1.7.8                        

• hypotesting: new parameter checks

                    Changes in version 1.7.6                        
  

• hypotesting: bug fix for MultiAssayExperiment objects

                    Changes in version 1.7.4                        
  

• writing: bug fix when writing MultiAssayExperiment with single colData column

                    Changes in version 1.7.2                        
  

• correcting: bug fix when removing features with 0 or NAs in all reference samples

PhyloProfile

                   Changes in version 1.20.0                        

• added UMAP clustering

• improved domain plot #110

• fast mode for large profile plot

• option to change font

• option to show gene names

• option to sort genes by defined list

• option to upload preprocessed data from an input folder

Pigengene

             Changes in version 1.31.2 (2024-06-21)                 

General

• Links to project.eigen were added in related fucntions docs.

Changes in existing functions

• doMinimize was added to compute.pigengene.

PIPETS

             Changes in version 1.1.5 (2024-09-27)                  

• Added strand specific analysis parameters. Can now use different threshAdjust and highOutlierTrim values for each strand should they choose.

             Changes in version 1.1.4 (2024-09-11)                  
  

• Resolved warnings that popped up during Initial Poisson Distribution testing. Results will not be greatly changed but now PIPETS correctly counts all reads.

• Fixed problems in Genomic Ranges input method so that it now correctly mirrors the analysis performed for bed file inputs.

             Changes in version 1.1.3 (2024-07-12)                  
  

• Changed read quality score parameter from a set value to a minimum, so anything equal to or greater than the input value will be considered

             Changes in version 1.1.2 (2024-07-11)                  
  

• Changed PIPETS to use read quality score as a cutoff instead of read length. Functions as better trimming process

• Input bed files and GRanges objects now both correctly use read quality score

• Updated Vignette file wording to properly match recent changes

             Changes in version 1.1.1 (2024-06-06)                  
  

• Resolved Git inconsistencies, made minor fixes

             Changes in version 1.1.0 (2024-05-14)                  
  

• Added Benjamini-Hochberg multiple testing correction to help reduce incidence of Type I error

plotgardener

                   Changes in version 1.11.2                        

NEW FEATURES

• plotgardener now supports .(m)cool files for Hi-C data! Functions for reading and extracting features from .(m)cool files include:
• readCool
• readCoolBpResolutions
• readCoolNorms

• readCoolChroms .(m)cool files can now be used with any Hi-C plotting function in place of .hic files or other data types.

                   Changes in version 1.11.1                        
  

BUG FIXES

• plotPairs and plotPairsArches check and swap order of anchors.

• plotTranscripts NULL label checking bug fix.

                   Changes in version 1.11.0                        
  

Version bump for Bioconductor 3.19 release.

PLSDAbatch

                    Changes in version 1.1.1                        

• Date: 2024-09-18
• Text: pca function clash
• Details: Avoid the clash of function pca() from vegan and mixOmics packages

PoDCall

             Changes in version 1.13.1 (2023-05-15)                 

• Made PoDCall compatible with multiplexed target assays (multiple target channels)

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)

POMA

                   Changes in version 1.15.17                       

• Analyzing data with random effects in PomaLimma
• Select outcome factor in PomaBoxplots, PomaDensity, and PomaOutliers
• Documentation improvements
• Introduces PomaEnrichment for gene set analysis
• Allows custom study designs in PomaDESeq

pRoloc

                    Changes in version 1.45                         

Changes in version 1.45.2

• pRolocmarkers() has a new version argument, to allow for new markers versions to be added.
• 14 new marker sets have been added to pRolocmarkers() under version = 2 (new default).
• Documentation for pRolocmarkers() has been updated to include a description of version = 2 markers.

Changes in version 1.45.1

• Import ‘mclust::estep*()’.

Changes in version 1.45.0

• New devel version

pRolocGUI

                    Changes in version 2.15                         

CHANGES IN VERSION 2.15.2

• Fix bug in compare app when selecting marker classes and plotting the map
• Change organlle profile plots to 25% and 75% quantiles

CHANGES IN VERSION 2.15.1

• Remap in aggregation app.

CHANGES IN VERSION 2.15.0

• New version for Bioc devel

ProtGenerics

                   Changes in version 1.37.1                        

• Add estimatePrecursorIntensity() generic.

PSMatch

                     Changes in version 1.9                         

PSMatch 1.9.1

• Fix check errors.

PSMatch 1.9.0

• New Bioc devel.

pwalign

                    Changes in version 1.2.0                        

• No significant changes in this version.

QDNAseq

             Changes in version 1.41.3 (2024-07-24)                 

Miscellaneous

• exportBins(…, format = “vcf”) did not add meta-data information for field END to the VCF file header.

             Changes in version 1.41.2 (2024-07-23)                 
  

Bug Fixes

• poolRuns() would give an error “Error in colMeans2(oldphenodata, cols = numericCols, useNames = FALSE) : Argument ‘x’ must be a matrix or a vector.”

             Changes in version 1.41.1 (2024-07-20)                 
  

Miscellaneous

• Fix markup typo in help(“exportBins”).

• Add package test for poolRuns().

QFeatures

                    Changes in version 1.15                         

QFeatures 1.15.2

• Fix typo in normalisation methods.

QFeatures 1.15.2

• Fix bug in QFeatures::longFormat() when rownames are numerical (reported upstream https://github.com/waldronlab/MultiAssayExperiment/issues/331).
• Starting New API unit test (see issue #214.

QFeatures 1.15.1

• Import reshape2::melt, required for MultiAssayExperiment::longFormat().

QFeatures 1.15.0

• New Bioc devel

qPLEXanalyzer

                   Changes in version 1.23.1                        

• Add coefCV to NAMESPACE

• Modify pcaPlot to allow user to omit the labelling

• Switch from gridExtra to patchwork in vignette

                   Changes in version 1.23.0                        
  

• Version bump for Bioconductor 3.20, no changes to package

RaggedExperiment

                   Changes in version 1.30.0                        

New features

• metadata argument added to RaggedExperiment constructor function (@LiNk-NY).

Bug fixes and minor improvements

• Ensure order is the same in both sparse and dense outputs of compactAssay (@csoneson, #30)

RAIDS

                    Changes in version 1.3.3                        

SIGNIFICANT USER-VISIBLE CHANGES

o More comprehensive vignette

                    Changes in version 1.3.2                        

SIGNIFICANT USER-VISIBLE CHANGES

o New functions inferAncestry(), inferAncestryGeneAware() and getRefSuperPop() to simplify ancestry inference

                    Changes in version 1.3.1                        

SIGNIFICANT USER-VISIBLE CHANGES

o New function createAccuracyGraph() that creates a graphic representation of the accuracy for different values of PCA dimensions and K-neighbors through all tested ancestries.

Rarr

                     Changes in version 1.5                         

• Fixed bug when creating an empty array with a floating datatype. The fill value would be interpreted as an integer by read_metadata() and create and array of the wrong type.
• Fixed bug in update_zarr_array() when NULL was provided to one or more dimensions in the index argument. This was parsed incorrectly and the underlying zarr was not modified.
• Fixed bug in reading 64-bit integer arrays compressed with ZLIB or LZ4. The calculated decompression buffer size was too small and reading would fail. (Thanks to Dan Auerbach for the report: https://github.com/grimbough/Rarr/issues/10)
• Added support for the ZarrArray S4 class and the DelayedArray framework.
• Improvements to read and write performance.

rBLAST

             Changes in version 1.1.1 (2024-04-30)                  

Changes

• Added description of how to deal with multi-part databases.

• Fixed package anchors in man pages.

                    Changes in version 1.1.0                        
  

Changes

• makeblastDB() gained parameters db_name, hash_index and verbose.

• added has_blast() and made tests, man page code and vignette code conditional.

• added blast_db_cache() and blast_db_get() to manage downloading BLAST DBs using BiocFileCache.

Rcpi

             Changes in version 1.41.3 (2024-09-09)                 

Improvements

• Added early dependency checks for pwalign in functions that use pairwise alignment. If certain dependency conditions can’t be met, the error is raised immediately, preventing unnecessary computation (#26).

• Replaced rjson with jsonlite to maintain compatibility with R < 4.4.0. The recent rjson update (v0.2.22 , 2024-08-20) requires R (>= 4.4.0), which would break builds on r-oldrel (#28).

             Changes in version 1.41.2 (2024-08-30)                 
  

Improvements

• Since Bioconductor 3.19 and Biostrings 2.72.0, the pairwise sequence alignment facilities have been moved from Biostrings into the pwalign package. For maximum compatibility, we now detect the installed Biostrings version at runtime and decide which package to use for pairwise alignment, without introducing pwalign as an additional hard dependency.

When calling calcTwoProtSeqSim() and calcParProtSeqSim(), if users have Biostrings >= 2.72.0 installed while pwalign is not installed, expect to see an explicit error in the results saying that pwalign is required and should be installed from Bioconductor.

             Changes in version 1.41.1 (2024-07-20)                 

Improvements

• Replaced RCurl with httr2 and curl for retrieving molecular and sequence data from web APIs. Updated the outdated API endpoint URLs for DrugBank and RCSB PDB (#18).
• inst/CITATION now uses bibentry() to replace citEntry() (#19).
• Fixed check notes on lost braces when running R CMD check under R 4.4.x (#21).

RCy3

                   Changes in version 2.26.0                        

• Added documentation & checks for super-long commands
  • suggest users to use commandsPost() when URI too long
• Bug fixes:
  • check for Inf and -Inf in double columns during loadTableData, #224
  • fix missing base.url in some functions
• Add test functions

ReactomePA

                   Changes in version 1.49.1                        

• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)

recount

                   Changes in version 1.31.2                        

SIGNIFICANT USER-VISIBLE CHANGES

• Remove warnings related to using coverage_matrix() or expressed_regions() on Windows as rtracklayer::import() does work with local BigWig files on that operating system. I’m not sure if it will work with remote BigWig files given that remote BigWig file access on other operating systems is not working due to https://github.com/lawremi/rtracklayer/issues/83 and related issues.

ResidualMatrix

                   Changes in version 1.16.0                        

• Minor change to the recommended way to call BiocSingular::runPCA(), to avoid block-processing when computing the center.

Rhtslib

                    Changes in version 3.2.0                        

• No significant changes in this version.

ribosomeProfilingQC

                   Changes in version 1.17.1                        

• allow DNAStringSet for genome.

ropls

                   Changes in version 1.37.6                        

• minor vignette update

                   Changes in version 1.37.4                        
  

• plot_score new name of the previous gg_scoreplot method

                   Changes in version 1.37.2                        
  

• gg_scoreplot: now handling the 1D or empty models

rWikiPathways

                   Changes in version 1.25.1                        

• bug fix: downloadPathwayArchive scrapes “File Name” column

S4Arrays

                    Changes in version 1.6.0                        

NEW FEATURES

• Add fast colsum() method for ordinary matrices.

• Define low-level generics:
  • subset_Array_by_logical_array()
  • subset_Array_by_Lindex()
  • subset_Array_by_Mindex()
  • subset_Array_by_Nindex() with default methods. Their purpose is to support subsetting ([) of Array derivatives and to make it easier for developers of Array extensions to implement subsetting for their objects. They are not intended to be used directly by the end user.
• Define low-level generics:
  • subassign_Array_by_logical_array()
  • subassign_Array_by_Lindex()
  • subassign_Array_by_Mindex()
  • subassign_Array_by_Nindex() with default methods. Their purpose is to support subassignment ([<-) of Array derivatives and to make it easier for developers of Array extensions to implement subassignment for their objects. They are not intended to be used directly by the end user.

SIGNIFICANT USER-VISIBLE CHANGES

• read_block() now uses SparseArray::extract_sparse_array() instead of DelayedArray::OLD_extract_sparse_array() behind the scene to extract and load sparse blocks from a sparse array-like object. As a consequence, sparse blocks are now returned as SparseArray objects (implemented in the SparseArray package) instead of SparseArraySeed objects (implemented in the DelayedArray package).

S4Vectors

                   Changes in version 0.44.0                        

BUG FIXES

• Make sure that internal helper coerceToSimpleList() always propagates the mcols.

SAIGEgds

                    Changes in version 2.4.1                        

• add an option load.balancing to seqAssocGLMM_SPA()

SCArray

                   Changes in version 1.14.0                        

• update according to DelayedArray(>= 0.31.5)

SCArray.sat

                    Changes in version 1.6.0                        

• update according to DelayedArray(>= 0.31.5)

scBubbletree

                   Changes in version 1.7.21                        

• new abstract

• new vignette

• new function: get_num_cell_tiles Changes after version 1.71.21 (17 Sep, 2024)

• scBubbletree paper accepted in BMC bioinformatics Changes after version 1.71.22 (20 Sep, 2024)

• simplified tree visualizations added in outout as object: tree_simple

                    Changes in version 1.7.2                        
  

• bubbletree comparison function get_bubbletree_comparison

• main functions simplified and defaults changed

• documentation updated

scDblFinder

             Changes in version 1.19.6 (2024-09-19)                 

• added a dbr.per1k parameter to set doublet rates per thousands of cells, updated the default from 1 to 0.8\%

• fixed some issues stemming from the cxds score in some corner cases (absence of inverse correlation between genes)

• updated documentation

scMultiSim

                    Changes in version 1.1.3                        

• Added the Shiny app to help users visualize the effect of each parameter and adjust the simulation options.
• Added the speed.up parameter to enable experimental speed optimization.

• Bug fixes and improvements.

                    Changes in version 1.1.0                        
  

Prepare for the Bioconductor release

• Fix build errors

scp

                    Changes in version 1.15                         

scp 1.15.2

• fix: fixed x-axis direction annotation for volcano plot on contrast
• fix: solved bug in DA when missing contrast level in modelled feature (issue #65).
• Add link to Leduc SCP.replication vignette.

scp 1.15.1

• test: added unit tests for scplainer: ScpModel-Class, scpModelFit-Class, ScpModel-Workflow

scp 1.15.0

• New Bioconductor 3.20 (devel) release

scran

                    Changes in version 1.34                         

• Bugfix for quickCluster() to pass along arguments to the internal per-block call.

scRNAseqApp

                   Changes in version 1.15.22                       

• add warning message to log file when the atac bigwig files are not available.

                   Changes in version 1.15.21                       
  

• fix a bug that counter table is not available.

                   Changes in version 1.15.20                       
  

• Add csv format for figure data download.

                   Changes in version 1.15.19                       
  

• Try to handle the error Timeout was reached: [www.ncbi.nlm.nih.gov] SSL/TLS connection timeout.

                   Changes in version 1.15.18                       
  

• add protection of column sampleID in cell info editor funcitons.

                   Changes in version 1.15.17                       
  

• Error handle if metadata contains ‘

  ’.

• add cell info editor funcitons.

                   Changes in version 1.15.16                       
  

• add more download format.

                   Changes in version 1.15.15                       
  

• fix the low resolution of the plot.

                   Changes in version 1.15.14                       
  

• fix the dotplot download issue.

                   Changes in version 1.15.13                       
  

• add detailed fontsize and font family control.

• change the dotplot from ggplot2 to complexheatmap.

                   Changes in version 1.15.12                       
  

• order the stacked violin plots by input order.

                   Changes in version 1.15.11                       
  

• add reorder function for splitBy for violin plots.

                   Changes in version 1.15.10                       
  

• add color picker.

• add splitBy for violin plots.

• fix the issue that refresh explorer will lost the subset info.

                   Changes in version 1.15.9                        
  

• add help video playlist.

                   Changes in version 1.15.8                        
  

• add functionality to allow different labels for cell info.

• allow subset groups for explorer.

                   Changes in version 1.15.7                        
  

• fix the issue of reload everything when edit the cell info.

                   Changes in version 1.15.6                        
  

• Editable cell info during login mode.

• Hiden the cells when check the hidden box.

                   Changes in version 1.15.5                        
  

• Response to the download width and height.

                   Changes in version 1.15.4                        
  

• Access tab via query string.

                   Changes in version 1.15.3                        
  

• Access data via data title.

                   Changes in version 1.15.2                        
  

• Add favicon.

                   Changes in version 1.15.1                        
  

• Fix the unique vistor counter.

scuttle

                    Changes in version 1.16                         

• addPerCellQCMetrics() will (optionally) add the feature subset identities to the row data of the SingleCellExperiment.

• Added uniquifyDataFrameByGroup() to collapse grouped rows in a DataFrame into their unique values.

SeqArray

                   Changes in version 1.46.0                        

UTILITIES

• seqGetData() return NULL, if ‘var.name=character()’

                   Changes in version 1.44.3                        
  

UTILITIES

• update the C codes according to ‘R_USE_STRICT_R_HEADERS=true’ & ‘R_CXX_USE_NO_REMAP=true’

                   Changes in version 1.44.2                        
  

BUG FIXES

• fix seqAddValue(, val=vector("list", NUM_VARIANT))

• fix the ploidy returned from seqVCF_Header(), when there are genotypes of males and females on Chromosome X

                   Changes in version 1.44.1                        
  

UTILITIES

• new option ‘numvariant’ in seqEmptyFile()

BUG FIXES

• seqMerge() should internally use “chr_position_ref_alt” to distinguish the variants in different files

• seqAddValue(, varnm="annotation/filter") should work with a factor variable

• seqAddValue(, varnm="variant.id") can reset the variant IDs with a different number of the variants

ShortRead

                    Changes in version 1.64                         

BUG FIXES

• (v 163.1) rely on system-provided zlib on all platforms

simplifyEnrichment

                    Changes in version 2.0.0                        

• use simona for semantic similarity calculation

• removed similarity functions for DO and based on overlaps (the count)

SingleCellAlleleExperiment

                    Changes in version 1.0.2                        

Fixed error in tests

                    Changes in version 1.0.1                        

Updated allele names in the vignette after data package “scaeData” was updated

SingleR

                    Changes in version 2.8.0                        

• Added the test.genes= argument to trainSingleR(), to restrict marker detection to only those genes in the test dataset. This is also checked against rownames(test) in classifySingleR() to ensure that the test’s feature space is consistent with the space used during training.

• The introduction of test.genes= means that we no longer need to explicitly subset the rows of the reference dataset (to match the test features) in SingleR(). This saves memory by avoiding an unnecessary copy of the reference dataset, but may also slightly alter the marker selection as ties are broken in a different way. Namely, if the top X genes are used as markers, and the X-th and (X+1)-th gene have the same log-fold change, tie breaking will be based on the ordering of the rows in the reference matrix - which is no longer the same as in the previous version of SingleR. This results in some slight differences in the markers that propagate down to the classification results.

• Restored the BNPARAM= argument in trainSingleR(), to enable more fine-grained specification of neighbor search algorithms. The approximate= argument is deprecated.

• Soft-deprecated check.missing= in classifySingleR() and combineRecomputedResults(). This is because any filtering will cause a mismatch between the row names of tests and the test.genes in trained. Rather, filtering should be done prior to trainSingleR(), as is done in the main SingleR() function.

• combineRecomputedResults() now supports fine-tuning to resolve closely-related labels from different references. This is similar to the fine-tuning in classifySingleR() where the feature space is iterately redefined as the union of markers of labels with near-highest scores.

• Added the plotMarkerHeatmap() function to plot a diagnostic heatmap of the most interesting markers for each label.

sketchR

                    Changes in version 1.1.3                        

• Update environment to avoid setuptools incompatibility

                    Changes in version 1.1.2                        
  

• Specify Linux aarch environment

                    Changes in version 1.1.1                        
  

• Update environments to adapt to basilisk conda update

smartid

                    Changes in version 1.1.2                        

• Update marker selection functions to fix wrong names of marker list.

                    Changes in version 1.1.1                        
  

• Update cal_score() function to convert input sparse matrix into dense matrix.

SNPRelate

                   Changes in version 1.38.1                        

UTILITIES

• update the C codes according to ‘R_USE_STRICT_R_HEADERS=true’ & ‘R_CXX_USE_NO_REMAP=true’

SpaceMarkers

                    Changes in version 1.1.3                        

• Optimized the long running row.dunn.test() function

• Corrected sparse -> dense conversions

                    Changes in version 1.1.2                        
  

• Added getPairwiseInteractingGenes which enables pairwise analysis of interacting patterns

                    Changes in version 1.1.1                        
  

• getSpatialFeatures: add default method to infer the object passed to it.

SparseArray

                    Changes in version 1.6.0                        

NEW FEATURES

• Linear subsetting of a SVT_SparseArray object e.g. svt[11:13].

• Add the ‘dim’ and ‘dimnames’ arguments to SVT_SparseArray() constructor function. Main use case is to make it easy and efficient to construct a zero-only SVT_SparseArray object of arbitrary dimensions.

• Add is_nonzero() generic with a default method and fast methods for SVT_SparseArray, COO_SparseArray, and sparseMatrix objects.

• The Sparse Vector Tree of a SVT_SparseArray can have “lacunar leaves”, that is, leaves where the nzvals are missing. These leaves are semantically equivalent to leaves where all the values in nzvals are ones. This reduces the memory footprint of a “logical” SVT_SparseArray with no NAs by half. Note that a “logical” SVT_SparseMatrix object with no NAs is similar to an ngCMatrix object from the Matrix package. ngCMatrix objects don’t store any non-zero values either (they’re implicitly considered to be TRUEs), only their offsets.

• col/row summarization methods (a.k.a. “matrixStats methods”) now work on COO_SparseArray objects (in addition to SVT_SparseArray objects).

• Add row/colSums2() and row/colMeans2() methods for SparseArray objects.

• rowsum(), crossprod(), tcrossprod(), and %*% methods now work on COO_SparseMatrix objects (in addition to SVT_SparseMatrix objects).

• Add fast colsum() methods for SparseMatrix and dgCMatrix objects.

• Add is.na(), is.nan(), and is.infinite() methods for SVT_SparseArray objects.

• Add pmin() and pmax() methods for SparseArray objects.

• aperm(<SVT_SparseArray>) now supports S4Arrays::aperm2() extended semantic. See ‘?S4Arrays::aperm2’ for details.

• Add ‘dimnames’ argument to randomSparseArray(), poissonSparseArray(), randomSparseMatrix(), and poissonSparseMatrix().

• Coercions from dgTMatrix, lgTMatrix, or ngTMatrix, to COO_SparseMatrix/Array or SVT_SparseMatrix/Array, and vice versa.

• Coercions from ng[C

  R

  T]Matrix to COO_SparseMatrix, and vice versa.

• Coercion from ngCMatrix to SVT_SparseMatrix, and vice versa.

• NaArray objects: WORK-IN-PROGRESS! New objects that use the same internal representation as SVT_SparseArray objects (Sparse Vector Tree), but background value is NA instead of zero. See https://github.com/fmicompbio/footprintR/issues/7 for the motivating use case. They support most operations supported by SVT_SparseArray objects: [, [<-, t(), aperm(), cbind(), rbind(), abind(), matrixStats operations (col(), row()), etc… What’s missing:
  • a dedicated vignette;
  • some row*() functions are not ready yet.
• Add new generics is_nonna(), nnacount(), nnawhich(), nnavals(), and nnavals<-(), with default methods and methods for NaArray objects.

SIGNIFICANT USER-VISIBLE CHANGES

• Refactored subassignment of a SVT_SparseArray object, which resulted in significant speed improvement and memory footprint reduction.

• Speed up some row summarization methods (e.g. rowSums(x)) by implementing them natively in C rather than doing a transposition followed by a column summarization (e.g. colSums(t(x))). This avoids the costly transposition step which is very time and memory consuming. Row summarization methods with native C implementation so far: rowAnyNAs() (35x speedup), rowMins() (6x speedup), rowMaxs() (6x speedup), rowSums() (20x speedup), rowMeans() (18x speedup), rowVars() (5x speedup), and rowSds() (5x speedup). More methods will follow.

• Special-case ‘lambda=0’ in poissonSparseArray() so the empty SVT_SparseArray object gets returned instantaneously.

BUG FIXES

• Fix integer overflow in nzwhich() methods for CsparseMatrix and RsparseMatrix objects when the object has a length >= 2^31.

• Fix bug in coercion from COO_SparseMatrix to [d|l]gCMatrix or [d|l]gRMatrix when the ‘nzcoo’ slot of the COO_SparseMatrix object contains duplicates.

• Make sure that coercion from CsparseMatrix to SVT_SparseMatrix works on any [d|l|n]gCMatrix derivative and not just on a [d|l|n]gCMatrix instance.

sparseMatrixStats

                    Changes in version 1.17                         

• Fix handling of missing values in rowSums2 if cols is a boolean vector

• Implement optimized code path for rowSums2 and rowMeans2 if cols is provided

SpatialFeatureExperiment

                    Changes in version 1.7.1                        

• Added image setter, Img<-
• Implemented spatial aggregation functions to aggregate directly from transcript spot file, from rowGeometry, or from cell geometries in SFE objects

• Implemented splitByCol to split SFE objects by geometry, splitSamples to split by sample_id, and splitContiguity to split by cotiguity of an annotGeometry

                    Changes in version 1.6.1                        
  

• readRDS converts old style SpatRasterImage to the new style
• readSelectTx and addSelectTx functions to read transcript spots from a few select genes from the parquet output of formatTxSpots or add them to an SFE object
• Added formatTxTech and addTxTech functions, basically thin wrappers of formatTxSpots and addTxSpots with presets for Vizgen, Xenium, and CosMX

spatialHeatmap

             Changes in version 2.11.4 (2024-07-28)                 

• Reduced dependencies.

             Changes in version 2.11.2 (2024-07-23)                 
  

• The function cvt_id accepts vectors.

             Changes in version 2.11.1 (2024-06-14)                 
  

• Fixed some contrasts in spatial enrichment.

Spectra

                    Changes in version 1.15                         

Changes in 1.15.13

• Add precursorMz<- method issue #336.

Changes in 1.15.12

• Add generic backendRequiredSpectraVariables() to allow definition of mandatory spectra variables for a backend.

Changes in 1.15.11

• Add reference to MsBackendMetaboLights.

Changes in 1.15.10

• Add new extractSpectra() generic and implementation for MsBackend. Fixes issue #5.

Changes in 1.15.9

• Restructure and reorganize documentation for Spectra.

Changes in 1.15.8

• Refactor the Spectra() constructor method: better support for initialization of backends that define their own specific parameters.

Changes in 1.15.7

• Change estimatePrecursorIntensity() to a method to avoid overrides/clashes with the same-named implementation in xcms.

Changes in 1.15.6

• Fix in selectSpectraVariables() for MsBackendMzR: ensure peaks variables “mz” and “intensity” are not by default removed.

Changes in 1.15.5

• Add new filterPeaksRanges() function to filter mass peaks by ranges on numeric spectra or peak variables.

Changes in 1.15.3

• For evaluation of the Spectra’s processing queue: call functions from the MetaboCoreUtils directly through their namespace (MsCoreUtils::) to avoid errors if performed in parallel on Windows machines or if called on a re-loaded object.
• New asDataFrame() function to convert a (small) Spectra object into a long DataFrame.

Changes in 1.15.2

• Add dataStorageDataPath() and dataStorageDataPath<- methods to allow updating/adapting the path of the data storage files of backends supporting that issue #321.

Changes in 1.15.1

• Improve documentation for combineSpectra() and combinePeaks() issue #320.

SPIAT

                    Changes in version 1.7.2                        

BUG FIXES

• Fixed cluster assignment issue in function identify_neighborhoods().

                    Changes in version 1.7.1                        
  

BUG FIXES

• Added feature_colname parameter to functions plot_cell_marker_levels() and marker_intensity_boxplot().

                    Changes in version 1.7.0                        
  

Development version on Bioconductor 3.20.

splatter

             Changes in version 1.30.0 (2024-10-30)                 

• Minor maintenance chores:

• Update roxygen2 version

• Remove old CI config files

• Add PR commands GitHub action

• Re-configure pkgdown site

• Add dependabot GitHub action

• Update README

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 1.35.1                        
  

• The long format for output from shiftCor

• The long format for input from statAnalysis

SummarizedExperiment

                   Changes in version 1.36.0                        

NEW FEATURES

• Calling saveRDS() on a SummarizedExperiment object that contains out-of-memory data now raises an error with a message that redirects the user to HDF5Array::saveHDF5SummarizedExperiment().

SIGNIFICANT USER-VISIBLE CHANGES

• Move documentation of constructor function SummarizedExperiment() from RangedSummarizedExperiment-class.Rd to SummarizedExperiment-class.Rd. See https://github.com/Bioconductor/SummarizedExperiment/issues/80

• Change default value of ‘rowData’ argument in SummarizedExperiment() constructor from GRangesList() to NULL.

BUG FIXES

• Fix typos in error message from assay() and assays() setters.

SVMDO

             Changes in version 1.5.5 (2024-08-30)                  

• Fixing enrichDO-related error
• Fixing deprecation issues about data table visualization in Shiny

SynExtend

                   Changes in version 1.17.7                        

• ExoLabel is much much faster and does a better job cleaning up when aborted early
• ExoLabel now has fewer arguments

• Updates to man pages

                   Changes in version 1.17.6                        
  

• Lots of internal improvements to ExoLabel to increase computational speed and decrease disk usage.
• ExoLabel will no longer crash if given relative paths.
• Adds more internal error checking to prevent some rare bugs.
• Updates man pages to reflect new changes.

• Updates EstimateExoLabel to reflect new changes.

                   Changes in version 1.17.5                        
  

• ExoLabel will no longer brick R during sorts on large files.
• ExoLabel reports more progress during some lengthy processing sections when verbose=TRUE

• Known issue: “Copying source file” step is still non-interruptable, will be fixed in a later update

                   Changes in version 1.17.4                        
  

• ExoLabel now allows an inflation argument to control application of inflation

                   Changes in version 1.17.3                        
  

• predict.EvoWeaver now supports returning p-values separately from raw score for some algorithms.

• OpenMP implementation for EvoWeaver algorithms that support it has been fixed

                   Changes in version 1.17.2                        
  

• RandForest function added to train random forest models
• Associated man pages for RandForest and DecisionTree objects
• New methods for DecisionTree objects to plot and coerce to dendrogram

• Small bugfix to subset.dendrogram

                   Changes in version 1.17.1                        
  

• Major updates to EvoWeaver:
• predict.EvoWeaver now returns a data.frame by default
• Method arguments are updated to match their names in the associated EvoWeaver manuscript
• Above changes have propagated to documentation files
• New Phylogenetic Profiling methods with improved accuracy
• New meta-methods PhylogeneticProfiling, PhylogeneticStructure, GeneOrganization, SequenceLevel for predict.EvoWeaver
• New pre-trained Ensemble models have been included
• Updates to ExoLabel for better status printing

TargetSearch

                    Changes in version 2.8.0                        

NEW FEATURES

• Allow incompatible data when combining objects tsLib and tsSample. The idea is if the column names of the data slots are different, the c operator do not fail. There are, however, limitations with some data types (like lists or matrices). If this is the case, then throw a more meaningful error message. (commit 6fb2f59)

BUG FIXES

• Fix FAMEoutliers manual grouping: The comparison should use character vectors instead of numeric. Also, an error was thrown due to an if condition not having an scalar return (due to using is.na). Note that since this version, the default values of startDay and endDay have been set as NULL. (commit 69e8a2f).

INTERNAL

• Add tests for FAMEoutliers.

                    Changes in version 2.6.2                        
  

BUG FIXES

• Use \providecommand for missing defines in vignettes instead

                    Changes in version 2.6.1                        
  

BUG FIXES

• Fix vignettes building by adding missing latex commands due to an incompatibility between BiocStyle and knitr

TBSignatureProfiler

                   Changes in version 1.17.0                        

Minor Changes

• Added Li_3 signature
• Adjusted function to create documentation in Signature Addition vignette
• Fixed Zhao_Nano_6 signature documentation

Bug Fixes

• Changed out .data pronouns to use proper tidyr variable calling

TENxIO

                    Changes in version 1.8.0                        

New features

• The import method for h5 files now includes all rowData which typically includes “ID”, “Symbol”, and “Type” columns.

Bug fixes and minor improvements

• rownames are set to first column in the features.tsv.gz data (rownames for h5 files are determined by HDF5Array::TENxMatrix)
• TENxH5 now tests whether there is a /matrix/features/interval dataset in the h5 file. It sets ranges to NA_character_ when interval data is not found.

tidySpatialExperiment

                    Changes in version 1.0.1                        

• Greatly improved interactive gating, facilitated via tidygate.

TileDBArray

                   Changes in version 1.16.0                        

• Minor fix for as.data.frame= deprecation in tiledb_array().

• Support other datatypes for the dimensions and storage when configuring a TileDBRealizationSink. This is achieved via the new storagetype= and dimtype= arguments. Also added getTileDBDimType() and setTileDBDimType() to globally define the choice of dimension datatype.

• Bugfix to TileDBArraySeed to correctly handle dimension domains that do not start at 1. This requires a modification to the class to record the domain offset.

• Added a offset= option to TileDBRealizationSink() to create arrays with dimension domains that do not start at 1. This requires a modification to the associated class to record the domain offset.

tomoseqr

             Changes in version 1.11.1 (2022-10-25)                 

• Made the following changes: o Added 3D visualize function to imageViewer o Changed normCount and normMask options in estimate3dExpressions() to normalize option. When it is TRUE (default), the function works as if normCount = "count", normMask = TRUE. When it is FALSE, the function works as if normCount = "none", normMask = FALSE.

trackViewer

                   Changes in version 1.41.10                       

• Improve the plot speed for interaction data.

                   Changes in version 1.41.9                        
  

• Add a simple gene track plot model.

                   Changes in version 1.41.8                        
  

• Add listNormalizations function.

                   Changes in version 1.41.7                        
  

• Fix the bug that newpage parameter not used for plotGRanges.

                   Changes in version 1.41.6                        
  

• Add legendPosition parameter for lollipop plot.

                   Changes in version 1.41.5                        
  

• Export the method $ for trackStyle class.

                   Changes in version 1.41.4                        
  

• Move the 3d plots to a different package.

                   Changes in version 1.41.3                        
  

• plot lolliplot with multiple shapes in one position.

                   Changes in version 1.41.2                        
  

• export view3dStructure function.

                   Changes in version 1.41.1                        
  

• Add mdsPlot function.

transmogR

                    Changes in version 1.1.1                        

• Added digestSalmon()

transomics2cytoscape

                   Changes in version 1.15.2                        

DATA or DOCUMENT CHANGES

• Update Version Information in vignette

                   Changes in version 1.15.1                        
  

DATA or DOCUMENT CHANGES

• Add inst/CITATION

treeclimbR

                    Changes in version 1.1.1                        

• Adapt unit tests to limma updates

treeio

                   Changes in version 1.29.2                        

• speedup read.beast() with multithreading supports (2024-10-27, Sun, #128)

                   Changes in version 1.29.1                        
  

• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)
• support treetime output (2024-07-18, Thu)
• https://treetime.readthedocs.io/en/latest/tutorials/clock.html

TVTB

             Changes in version 1.31.2 (2024-07-05)                 

Bug fix

• Fix tSVE() shiny application.

             Changes in version 1.31.1 (2024-07-04)                 
  

Bug fix

• Copy parseCSQToGRanges from ensemblVEP

txdbmaker

                    Changes in version 1.2.0                        

SIGNIFICANT USER-VISIBLE CHANGES

• Adjust makeTxDbFromBiomart() examples to reflect breaking change in Ensembl 113. See commit a5a885d for the details.

BUG FIXES

• Small fix to internal helper .Ensembl_getMySQLCoreDir(). See commit aa586a6 for the details.

tximeta

                   Changes in version 1.23.5                        

• GENCODE 47 (H.s.), M36 (M.m), and Ensembl 113

                   Changes in version 1.23.1                        
  

• GENCODE 46 (H.s.), M35 (M.m), and Ensembl 112

UCSC.utils

                    Changes in version 1.2.0                        

• No significant changes in this version.

universalmotif

                   Changes in version 1.22.3                        

• Fixed make_DBscores() crash.

                   Changes in version 1.22.2                        
  

• Added CITATION file.

                   Changes in version 1.22.1                        
  

BUG FIXES

• Always check object sizes before indexing in universalmotif_cpp(). Fixes build timeouts on Bioconductor.

updateObject

                   Changes in version 1.10.0                        

• No changes in this version.

variancePartition

                   Changes in version 1.35.4                        

• June 13, 2024

• fix bug in [.MArrayLM2 dropping residuals to a vector

                   Changes in version 1.35.3                        
  

• June 11, 2024

• in mvTest() with shrink.cov = TRUE uses lambda = 0.01

                   Changes in version 1.35.2                        
  

• June 6, 2024

• in mvTest() return beta and se

                   Changes in version 1.35.1                        
  

• May 31, 2024
• version bump for BioC

velociraptor

                   Changes in version 1.15.13                       

• Add separate environment (untested) for Linux Aarch64. Cannot break that platform more than it already is.

                   Changes in version 1.15.12                       
  

• Update Conda environment for Linux to avoid Anaconda channel.

                   Changes in version 1.15.11                       
  

• Re-enable plotVelocityStream() with a warning.

                   Changes in version 1.15.10                       
  

• Temporarily disable plotVelocityStream() due to unexplained issue related to metr::geom_streamline()

                   Changes in version 1.15.9                        
  

• Update Conda environment for Linux and MacOSX Arm.

• Patch GitHub Action to use GitHub version of remotes.

                   Changes in version 1.15.8                        
  

• Update Conda environment using micromamba for MacOSX Arm.

• Fix switch between MacOSX and MacOSX Arm environments.

                   Changes in version 1.15.7                        
  

• Update Conda environment using micromamba for Windows.

                   Changes in version 1.15.6                        
  

• Update Conda environment to use anaconda channel on Linux. Passed GitHub Action https://github.com/kevinrue/velociraptor/actions/runs/10612115572/job/29413105915.

                   Changes in version 1.15.5                        
  

• Update Conda environment to svelo==0.3.2 on Linux.

                   Changes in version 1.15.4                        
  

• Set scvelo version triggering deprecation error to 0.3.1.

                   Changes in version 1.15.3                        
  

• Revert environment for Linux to the one of Bioconductor release 3.18.

                   Changes in version 1.15.2                        
  

• Add environment for macOS (Intel); same environment as macos (M1).

                   Changes in version 1.15.1                        
  

• Fix issue #63.
• Update scvelo to 0.3.2 (conda-forge) for macOS (M1) and Linux.
• Update scvelo to 0.2.5 (bioconda) for Windows.
• Add mechanism to switch Conda environment (and scvelo version) based on operating system and architecture.
• Use scanpy.pp.neighbors to calculate neighbors due to deprecation of automatic neighbor calculation in scvelo.pp.moments.
• Update vignette to document the change of default value for n_neighbors from scvelo (30) to scanpy (15).

VisiumIO

                    Changes in version 1.2.0                        

New features

• Support VisiumHD file formats including parquet.
• Include format argument for h5 file imports (default remains mtx).
• Add example data for Visium and VisiumHD imports.

Voyager

                    Changes in version 1.7.2                        

• Fixed bug that caused error when computing Lee’s L on DelayedArray

                    Changes in version 1.7.1                        
  

• Revamped user interface of plotGeometry to allow plotting multiple col, row, and annot geometries at once
• Allow plotting transcript spots in plotGeometry, plotSpatialFeature, plotLocalResult, and spatialReducedDim

xcms

                     Changes in version 4.3                         

Changes in version 4.3.3

• Fix issue #755: chromatogram() with msLevel = 2 fails to extract chromatographic data if isolationWindowTargetMz is not specified or available (e.g. for MSe data).
• Support coercing from XcmsExperiment to XCMSnExp with as(object, “XCMSnExp”).
• Change estimatePrecursorIntensity() to a method and add an implementation for MsExperiment objects.

Changes in version 4.3.2

• Remove data/results import/export functionality as it is being developed in the MsIO package.

Changes in version 4.3.1

• Support excluding samples or sample groups from defining features with PeakDensity correspondence analysis (issue #742).
• Add plotPrecursorIons() function.
• Fix in dropFeatureDefinitions() that was not correctly removing additional metadata from gap-filled chromatographic peaks.

NEWS from existing Data Experiment Packages

CardinalWorkflows

                   Changes in version 1.37.1                        

BUG FIXES

• Updates for Cardinal v3.8

curatedPCaData

             Changes in version 1.1.1 (2024-05-28)                  

• Minor fixes for Imports/Suggests for vignettes

gDRtestData

          Changes in version 22023-05-15 (2023-05-15)               

• fix related with data.table

           Changes in version 2024-07-09 (2024-07-09)               
  

• reprocess datasets as per new columns added into Metrics assay

geneLenDataBase

                   Changes in version 1.42.0                        

• Role of maintainer taken over by Federico Marini

• Refreshing the codebase, introducing roxygen-based documentation and applying styler for consistent spacing, as well as using Github Actions for CI/CD

JohnsonKinaseData

                    Changes in version 1.1.1                        

• Version bump

                    Changes in version 1.1.0                        
  

• Added tyrosine kinase PWMs published in Yaron-Barir et al. 2024

• Added option to mach acceptor specificity

• Added upstream/downstream options to flexibly trim phospho-peptides

MetaScope

                    Changes in version 3.19                         

Bug Fixes

• Identified the Rbowtie2 parameter k as being doubled when specified for bowtie filter or align steps.

• Added another call to taxize in convert_animalcules() to catch any accessions that were not mapped to a UID in metascope_id(), in addition to another call in metascope_id() itself

Major changes

• Altered bt2_params objects to reflect 98% identity (16S), 95% identity (metagenomics) and added a parameter for when the origin genome is thought to not be present in the reference database.

• Added SILVA species_headers object called internally in convert_animalcules_silva

• Added convert_animalcules_silva function

                    Changes in version 3.18                         
  

Bug Fixes

• Fixed taxonomy table function to output correctly formatted table

• Fixed examples for various functions that were calling genomes with download_refseq but genomes were not able to be found.

• Fixed plot generation for metascope_id()

• Fixed premature stopping of download_refseq for strains labeled as “no rank” in NCBI.

• Fixed identification of reads as unknown genomes (due to outdated reference databases that identify genomes now removed from NCBI). The unknown genomes will now be distinctly identified based on NCBI accession ID, which will separate them in the final results. IDs can also be looked up manually (on NCBI website) to see what the reads were aligning to.

• Incorporated unknown taxa (removed from NCBI databases) into output of convert_animalcules()

Major changes

• Added ability to identify reads from databases other than NCBI (known to work for Silva and Greengenes2)

MicrobiomeBenchmarkData

             Changes in version 1.7.1 (2021-09-26)                  

• Added a function (scml) for re-calibrating the “Stammler_2016_16S_spikein” dataset with SCML: spike-in-based calibration to total microbial load.

microbiomeDataSets

             Changes in version 1.13.2 (2024-06-26)                 

• LahtiWAData removed

• HintikkAXOData removed

pRolocdata

                   Changes in version 1.43.1                        

• move content of inst/extdata to the pRolocdata dataverse (https://dataverse.uclouvain.be/dataverse/pRolocdata).

                   Changes in version 1.43.0                        
  

• new devel version

scaeData

                    Changes in version 1.1.2                        

• Lookup tables have been updated to reflect complete allele names

                    Changes in version 1.1.1                        
  

• Changed filter_mode parameter value in the vignette to avoid check error

scATAC.Explorer

                   Changes in version 1.12.0                        

• corrected a bug when searching in-between years

• added h5ad support to saveATAC()

• added more examples in the help documentation for queryATAC()

scMultiome

                    Changes in version 1.4.2                        

• replace writeSparseMatrix with alabaster.matrix::writeSparseMatrix

scRNAseq

                   Changes in version 2.20.0                        

• Support complex queries in searchDatasets() via a human-friendly syntax.

SpatialDatasets

             Changes in version 1.5.0 (2022-04-27)                  

• reformat datasets to SpatialExperiment version 1.5.3

             Changes in version 1.3.3 (2022-01-31)                  
  

• add new datasets ST_mouseOB, SlideSeqV2_mouseHPC

• reformat datasets to SpatialExperiment version 1.5.2

spatialLIBD

                   Changes in version 1.17.6                        

BUG FIXES

• Fixed the bug reported by @lahuuki about vis_grid_clus() not handling logical() cluster variables. See https://github.com/LieberInstitute/spatialLIBD/issues/80. To resolve this, sort_clusters() and get_colors() had to change internally. Examples and documentation for both functions have now been updated to showcase what happens when you provide a logical() vector as an input.

                   Changes in version 1.17.5                        
  

NEW FEATURES

• Added add_qc_metrics() inspired by https://github.com/LieberInstitute/Visium_SPG_AD/blob/master/code/07_spot_qc/01_qc_metrics_and_segmentation.R which adds seven new columns to the colData(spe) that can be useful when performing quality control of the data. Developed by @lahuuki.

                   Changes in version 1.17.3                        
  

NEW FEATURES

• Added support for SpatialExperiment objects created with visiumStitched::build_spe() https://research.libd.org/visiumStitched/reference/build_spe.html that stitch together multiple Visium capture areas. Developed by @Nick-Eagles.

NEWS from existing Workflows

recountWorkflow

                   Changes in version 1.29.2                        

SIGNIFICANT USER-VISIBLE CHANGES

• Implement a workaround to https://github.com/lawremi/rtracklayer/issues/83 which currently is limiting the ability to remotely access BigWig files using rtracklayer::import(). This affects the functions recount::expressed_regions(), recount::coverage_matrix(), and derfinder::getRegionCoverage() used in recountWorkflow.

Deprecated and Defunct Packages

SOFTWARE:

Sixty five software packages were removed from this release (after being deprecated in Bioc 3.19):

• BDMMAcorrect, beadarraySNP, BHC, biodbLipidmaps, BioNetStat, CancerInSilico, CancerSubtypes, cellHTS2, CNVgears, compartmap, contiBAIT, CoRegNet, CORREP, crisprseekplus, dpeak, EBSeqHMM, eegc, enrichTF, ensemblVEP, exomePeak2, farms, FCBF, flowMap, FoldGO, FScanR, FunChIP, GOSim, HumanTranscriptomeCompendium, ImmuneSpaceR, InterMineR, IntOMICS, IRISFGM, iterClust, maigesPack, metagene, MetaVolcanoR, miRmine, MMAPPR2, MobilityTransformR, multiOmicsViz, NeighborNet, oneSENSE, openPrimeRui, pathVar, pcxn, PERFect, phemd, PloGO2, proteasy, PSEA, pwOmics, RefPlus, ReQON, restfulSE, RIPAT, RLSeq, SimBindProfiles, SMAP, sparseDOSSA, SpidermiR, SQUADD, StarBioTrek, STROMA4, TimiRGeN, TNBC.CMS

• Please note: DNABarcodes, cliqueMS, CoSIA, NetPathMiner, and TnT, previously announced as deprecated in 3.19, have been updated and remain in Bioconductor.

Twenty One software packages are deprecated in this release and will be removed in Bioc 3.21:

• ATACCoGAPS, BiocOncoTK, biodbExpasy, biodbKegg, brainflowprobes, BRGenomics, CellaRepertorium, HTqPCR, microbiomeMarker, MQmetrics, nanotatoR, netOmics, Pi, polyester, psygenet2r, RandomWalkRestartMH, rDGIdb, Risa, RNAinteract, single, SummarizedBenchmark

EXPERIMENT DATA:

Four experimental data packages were removed from this release (after being deprecated in BioC 3.19):

• MMAPPR2data, pcxnData, restfulSEData, RLHub

• Please note: CoSIAdata, previously announced as deprecated in 3.19, has been updated and remain in Bioconductor.

Two experimental data packages are deprecated in this release and will be removed in Bioc 3.21:

• DmelSGI, RNAinteractMAPK

ANNOTATION DATA:

One annotation package was removed from this release:

• MafH5.gnomAD.v3.1.2.GRCh38

No annotation packages are deprecated in this release.

WORKFLOWS:

No workflow packages were removed from this release.

No workflow packages were deprecated in this release.

BOOKS:

No books were removed from this release.

No books were deprecated in this release.