DRIMSeq

This is the released version of DRIMSeq; for the devel version, see DRIMSeq.

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

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DOI: 10.18129/B9.bioc.DRIMSeq

Bioconductor version: Release (3.22)

The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.

Author: Malgorzata Nowicka [aut, cre]

Maintainer: Malgorzata Nowicka <gosia.nowicka.uzh at gmail.com>

Citation (from within R, enter citation("DRIMSeq")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("DRIMSeq")

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("DRIMSeq")

Differential transcript usage and transcript usage QTL analyses in RNA-seq with the DRIMSeq package PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, ImmunoOncology, MultipleComparison, RNASeq, SNP, Sequencing, Software, WorkflowStep

Version 1.38.0

In Bioconductor since BioC 3.3 (R-3.3) (9.5 years)

License GPL (>= 3)

Depends R (>= 3.4.0)

Imports utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2

System Requirements

URL

Suggests PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat

Linking To

Enhances

Depends On Me rnaseqDTU

Imports Me BANDITS

Suggests Me

Links To Me

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DRIMSeq_1.38.0.tar.gz

Windows Binary (x86_64) DRIMSeq_1.37.0.zip (64-bit only)

macOS Binary (x86_64) DRIMSeq_1.38.0.tgz

macOS Binary (arm64) DRIMSeq_1.38.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/DRIMSeq

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DRIMSeq

Bioc Package Browser https://code.bioconductor.org/browse/DRIMSeq/

Package Short Url https://bioconductor.org/packages/DRIMSeq/

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