Package: DRIMSeq 1.41.0

Malgorzata Nowicka

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

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.

Authors:Malgorzata Nowicka [aut, cre]

DRIMSeq_1.41.0.tar.gz
DRIMSeq_1.41.0.zip(r-4.7)DRIMSeq_1.41.0.zip(r-4.6)DRIMSeq_1.41.0.zip(r-4.5)
DRIMSeq_1.41.0.tgz(r-4.6-any)DRIMSeq_1.41.0.tgz(r-4.5-any)
DRIMSeq_1.41.0.tar.gz(r-4.7-any)DRIMSeq_1.41.0.tar.gz(r-4.6-any)
DRIMSeq_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DRIMSeq/json (API)
NEWS

# Install 'DRIMSeq' in R:
install.packages('DRIMSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:DRIMSeq-1.41.0(bioc 3.24)DRIMSeq-1.40.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologysnpalternativesplicingdifferentialsplicinggeneticsrnaseqsequencingworkflowstepmultiplecomparisongeneexpressiondifferentialexpression

7.05 score 2 packages 189 scripts 737 downloads 17 mentions 28 exports 43 dependencies

Last updated from:47ade4497c. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING172
linux-devel-x86_64WARNING292
source / vignettesOK356
linux-release-x86_64WARNING289
macos-release-arm64WARNING159
macos-oldrel-arm64WARNING310
windows-develWARNING304
windows-releaseWARNING239
windows-oldrelWARNING236
wasm-releaseOK154

Exports:coefficientscolnamescolnames<-common_precisioncommon_precision<-countsdesigndmDSdatadmFilterdmFitdmPrecisiondmSQTLdatadmTestelementNROWSgenewise_precisiongenewise_precision<-mean_expressionncolnrowplotDataplotPrecisionplotProportionsplotPValuesproportionsresultsrownamesrownames<-samples

Dependencies:BHBiocGenericsBiocParallelclicodetoolscpp11edgeRfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSplyrR6RColorBrewerRcppreshape2rlangS4VectorsS7scalesSeqinfosnowstatmodstringistringrvctrsviridisLitewithr

Differential transcript usage and transcript usage QTL analyses in RNA-seq with the DRIMSeq package

Rendered fromDRIMSeq.Rnwusingknitr::knitron May 30 2026.

Last update: 2017-08-22
Started: 2016-03-23

Readme and manuals

Help Manual

Help pageTopics
Plot the frequency of present featuresdm_plotDataDSInfo
Plot feature proportionsdm_plotProportions
Create dmDSdata objectdmDSdata
dmDSdata objectcounts,dmDSdata-method dmDSdata-class length,dmDSdata-method names,dmDSdata-method samples samples,dmDSdata-method [,dmDSdata,ANY-method [,dmDSdata-method
dmDSfit objectcoefficients,dmDSfit-method design,dmDSfit-method dmDSfit-class proportions proportions,dmDSfit-method
dmDSprecision objectcommon_precision common_precision,dmDSprecision-method common_precision<- common_precision<-,dmDSprecision-method design,dmDSprecision-method dmDSprecision-class genewise_precision genewise_precision,dmDSprecision-method genewise_precision<- genewise_precision<-,dmDSprecision-method mean_expression mean_expression,dmDSprecision-method
dmDStest objectdesign,dmDStest-method dmDStest-class results results,dmDStest-method
FilteringdmFilter dmFilter,dmDSdata-method dmFilter,dmSQTLdata-method
Fit the Dirichlet-multinomial and/or the beta-binomial full model regressiondmFit dmFit,dmDSprecision-method dmFit,dmSQTLprecision-method
Estimate the precision parameter in the Dirichlet-multinomial modeldmPrecision dmPrecision,dmDSdata-method dmPrecision,dmSQTLdata-method
Create dmSQTLdata objectdmSQTLdata
dmSQTLdata objectcounts,dmSQTLdata-method dmSQTLdata-class length,dmSQTLdata-method names,dmSQTLdata-method samples,dmSQTLdata-method [,dmSQTLdata,ANY-method [,dmSQTLdata-method
dmSQTLfit objectdmSQTLfit-class
dmSQTLprecision objectcommon_precision,dmSQTLprecision-method dmSQTLprecision-class genewise_precision,dmSQTLprecision-method mean_expression,dmSQTLprecision-method
dmSQTLtest objectdmSQTLtest-class results,dmSQTLtest-method
Likelihood ratio test to detect differential transcript/exon usagedmTest dmTest,dmDSfit-method dmTest,dmSQTLfit-method
MatrixList object$,MatrixList-method colnames,MatrixList-method colnames<-,MatrixList-method dim,MatrixList-method elementNROWS,MatrixList-method length,MatrixList-method MatrixList-class names,MatrixList-method names<-,MatrixList-method ncol,MatrixList-method nrow,MatrixList-method rownames,MatrixList-method rownames<-,MatrixList-method [,MatrixList,ANY-method [,MatrixList-method [[,MatrixList-method
Plot data summaryplotData plotData,dmDSdata-method plotData,dmSQTLdata-method
Precision versus mean expression plotplotPrecision plotPrecision,dmDSprecision-method plotPrecision,dmSQTLprecision-method
Plot feature proportionsplotProportions plotProportions,dmDSfit-method plotProportions,dmSQTLfit-method
Plot p-value distributionplotPValues plotPValues,dmDStest-method plotPValues,dmSQTLtest-method