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DRIMSeq

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


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, ImmunoOncology, MultipleComparison, RNASeq, SNP, Sequencing, Software, WorkflowStep
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
See More
Suggests PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat
Linking To
Enhances
Depends On Me rnaseqDTU
Imports Me BANDITS
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package DRIMSeq_1.30.0.tar.gz
Windows Binary DRIMSeq_1.30.0.zip
macOS Binary (x86_64) DRIMSeq_1.30.0.tgz
macOS Binary (arm64) DRIMSeq_1.30.0.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/
Package Downloads Report Download Stats