To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DRIMSeq")

In most cases, you don't need to download the package archive at all.

DRIMSeq

DOI: 10.18129/B9.bioc.DRIMSeq    

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

Bioconductor version: Release (3.6)

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 at uzh.ch>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DRIMSeq")

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, MultipleComparison, RNASeq, SNP, Sequencing, Software, WorkflowStep
Version 1.6.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 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
Imports Me IsoformSwitchAnalyzeR
Suggests Me
Build Report  

Package Archives

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

Source Package DRIMSeq_1.6.0.tar.gz
Windows Binary DRIMSeq_1.6.0.zip
Mac OS X 10.11 (El Capitan) DRIMSeq_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DRIMSeq
Package Short Url http://bioconductor.org/packages/DRIMSeq/
Package Downloads Report Download Stats

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