DOI: 10.18129/B9.bioc.DRIMSeq    

This package is for version 3.8 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: 3.8

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")):


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PDF R Script Differential transcript usage and transcript usage QTL analyses in RNA-seq with the DRIMSeq package
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biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, ImmunoOncology, MultipleComparison, RNASeq, SNP, Sequencing, Software, WorkflowStep
Version 1.10.1
In Bioconductor since BioC 3.3 (R-3.3) (3 years)
License GPL (>= 3)
Depends R (>= 3.4.0)
Imports utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2
Suggests PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat
Depends On Me rnaseqDTU
Imports Me IsoformSwitchAnalyzeR
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package DRIMSeq_1.10.1.tar.gz
Windows Binary DRIMSeq_1.10.1.zip
Mac OS X 10.11 (El Capitan) DRIMSeq_1.10.1.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 http://bioconductor.org/packages/DRIMSeq/
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