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>

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