DOTSeq
This is the released version of DOTSeq; for the devel version, see DOTSeq.
Genome-wide Detection of Differential ORF Usage
Bioconductor version: Release (3.23)
Differential open reading frame (ORF) translation analysis framework for ribosome profiling (Ribo-seq) with matched RNA-seq. Implements (i) Differential ORF Usage (DOU), a beta-binomial generalized linear model that models the expected proportion of Ribo-seq versus RNA-seq reads mapping to each ORF within a gene, and (ii) ORF-level Differential Translation Efficiency (DTE), a negative binomial GLM that capture changes in translation efficiency of individual ORFs across experimental conditions. Supports ORF-level read summarization for bulk and single-cell Ribo-seq.
Author: Chun Shen Lim [aut, cre] 
, Gabrielle Chieng [aut, ctb] , Marsden [fnd]
Maintainer: Chun Shen Lim <lim.bioinfo at gmail.com>
citation("DOTSeq")):Chun Shen Lim, Gabrielle Chieng. DOTSeq: Genome-wide Detection of Differential ORF Usage. doi:10.18129/B9.bioc.DOTSeq, R package version 1.0.0, https://bioconductor.org/packages/DOTSeq.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DOTSeq")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DOTSeq")| DOTSeq: Detecting Differential ORF Usage in Ribosome Profiling Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, DifferentialExpression, GeneExpression, GeneRegulation, Genetics, MultipleComparison, RNASeq, Regression, RiboSeq, Sequencing, SingleCell, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | ashr, boot, data.table, emmeans, glmmTMB, Matrix, methods, Rcpp, stats, utils, graphics, grDevices, pbapply, AnnotationDbi, BiocGenerics, BiocParallel, Biostrings, BSgenome, txdbmaker, DESeq2, GenomicAlignments, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicRanges, IRanges, rtracklayer, Rsamtools, S4Vectors, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/compgenom/DOTSeq |
| Bug Reports | https://github.com/compgenom/DOTSeq/issues |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, org.Hs.eg.db, curl, pasillaBamSubset, BiocStyle, biomaRt, DHARMa, eulerr, ggplot2, ggsignif, knitr, rmarkdown, testthat, withr, magick |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DOTSeq_1.0.0.tar.gz |
| Windows Binary (x86_64) | DOTSeq_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | DOTSeq_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | DOTSeq_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DOTSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DOTSeq |
| Package Short Url | https://bioconductor.org/packages/DOTSeq/ |
| Package Downloads Report | Download Stats |