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Bioconductor - DRIMSeq (development version)

DRIMSeq

This is the development version of DRIMSeq; for the stable release version, see DRIMSeq.

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

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.37.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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 Package Archives

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

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