DRIMSeq

DOI: 10.18129/B9.bioc.DRIMSeq    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DRIMSeq.

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

Bioconductor version: 3.9

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 "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, ImmunoOncology, MultipleComparison, RNASeq, SNP, Sequencing, Software, WorkflowStep
Version 1.12.0
In Bioconductor since BioC 3.3 (R-3.3) (3.5 years)
License GPL (>= 3)
Depends R (>= 3.4.0)
Imports utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2
LinkingTo
Suggests PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me rnaseqDTU
Imports Me BANDITS, IsoformSwitchAnalyzeR
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package DRIMSeq_1.12.0.tar.gz
Windows Binary DRIMSeq_1.12.0.zip
Mac OS X 10.11 (El Capitan) DRIMSeq_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DRIMSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DRIMSeq
Package Short Url https://bioconductor.org/packages/DRIMSeq/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: