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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DRIMSeq")
AuthorMalgorzata Nowicka [aut, cre]
Bioconductor views AlternativeSplicing DifferentialExpression DifferentialSplicing GeneExpression Genetics MultipleComparison RNASeq SNP Sequencing WorkflowStep
Date of publicationNone
MaintainerMalgorzata Nowicka <gosia.nowicka@uzh.ch>
LicenseGPL (>= 3)
Version1.4.0

View on Bioconductor

Functions

coefficients,dmDSfit-method Man page
colnames<-,MatrixList-method Man page
colnames,MatrixList-method Man page
common_precision Man page
common_precision<- Man page
common_precision<-,dmDSprecision-method Man page
common_precision,dmDSprecision-method Man page
common_precision,dmSQTLprecision-method Man page
counts,dmDSdata-method Man page
counts,dmSQTLdata-method Man page
design,dmDSfit-method Man page
design,dmDSprecision-method Man page
design,dmDStest-method Man page
dim,MatrixList-method Man page
dmDSdata Man page
[,dmDSdata,ANY-method Man page
dmDSdata-class Man page
[,dmDSdata-method Man page
dmDSfit-class Man page
dmDSprecision-class Man page
dmDStest-class Man page
dmFilter Man page
dmFilter,dmDSdata-method Man page
dmFilter,dmSQTLdata-method Man page
dmFit Man page
dmFit,dmDSprecision-method Man page
dmFit,dmSQTLprecision-method Man page
dm_plotDataDSInfo Man page
dm_plotProportions Man page
dmPrecision Man page
dmPrecision,dmDSdata-method Man page
dmPrecision,dmSQTLdata-method Man page
dmSQTLdata Man page
[,dmSQTLdata,ANY-method Man page
dmSQTLdata-class Man page
[,dmSQTLdata-method Man page
dmSQTLfit-class Man page
dmSQTLprecision-class Man page
dmSQTLtest-class Man page
dmTest Man page
dmTest,dmDSfit-method Man page
dmTest,dmSQTLfit-method Man page
elementNROWS,MatrixList-method Man page
genewise_precision Man page
genewise_precision<- Man page
genewise_precision<-,dmDSprecision-method Man page
genewise_precision,dmDSprecision-method Man page
genewise_precision,dmSQTLprecision-method Man page
length,dmDSdata-method Man page
length,dmSQTLdata-method Man page
length,MatrixList-method Man page
[,MatrixList,ANY-method Man page
MatrixList-class Man page
[,MatrixList-method Man page
[[,MatrixList-method Man page
$,MatrixList-method Man page
mean_expression Man page
mean_expression,dmDSprecision-method Man page
mean_expression,dmSQTLprecision-method Man page
names,dmDSdata-method Man page
names,dmSQTLdata-method Man page
names<-,MatrixList-method Man page
names,MatrixList-method Man page
ncol,MatrixList-method Man page
nrow,MatrixList-method Man page
plotData Man page
plotData,dmDSdata-method Man page
plotData,dmSQTLdata-method Man page
plotPrecision Man page
plotPrecision,dmDSprecision-method Man page
plotPrecision,dmSQTLprecision-method Man page
plotProportions Man page
plotProportions,dmDSfit-method Man page
plotProportions,dmSQTLfit-method Man page
plotPValues Man page
plotPValues,dmDStest-method Man page
plotPValues,dmSQTLtest-method Man page
proportions Man page
proportions,dmDSfit-method Man page
results Man page
results,dmDStest-method Man page
results,dmSQTLtest-method Man page
rownames<-,MatrixList-method Man page
rownames,MatrixList-method Man page
samples Man page
samples,dmDSdata-method Man page
samples,dmSQTLdata-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/DRIMSeq.R R/class_MatrixList.R R/class_dmDSdata.R R/class_dmDSfit.R R/class_dmDSprecision.R R/class_dmDStest.R R/class_dmSQTLdata.R R/class_dmSQTLfit.R R/class_dmSQTLprecision.R R/class_dmSQTLtest.R R/class_show_utils.R R/dmDS_CRadjustment.R R/dmDS_estimateCommonPrecision.R R/dmDS_estimateTagwisePrecision.R R/dmDS_filter.R R/dmDS_fit.R R/dmDS_profileLik.R R/dmSQTL_CRadjustment.R R/dmSQTL_estimateCommonPrecision.R R/dmSQTL_estimateTagwisePrecision.R R/dmSQTL_filter.R R/dmSQTL_fit.R R/dmSQTL_permutations.R R/dmSQTL_profileLik.R R/dm_CRadjustmentManyGroups.R R/dm_CRadjustmentOneGroup.R R/dm_CRadjustmentRegression.R R/dm_LRT.R R/dm_core_Hessian.R R/dm_core_colorb.R R/dm_core_deviance.R R/dm_core_lik.R R/dm_core_score.R R/dm_estimateMeanExpression.R R/dm_fitManyGroups.R R/dm_fitOneGroup.R R/dm_fitRegression.R R/dm_plotData.R R/dm_plotPrecision.R R/dm_plotProportions.R R/dm_plotPvalues.R R/dm_profileLikModeration.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/DRIMSeq.R
inst/doc/DRIMSeq.Rnw
inst/doc/DRIMSeq.pdf
man
man/MatrixList-class.Rd man/dmDSdata-class.Rd man/dmDSdata.Rd man/dmDSfit-class.Rd man/dmDSprecision-class.Rd man/dmDStest-class.Rd man/dmFilter.Rd man/dmFit.Rd man/dmPrecision.Rd man/dmSQTLdata-class.Rd man/dmSQTLdata.Rd man/dmSQTLfit-class.Rd man/dmSQTLprecision-class.Rd man/dmSQTLtest-class.Rd man/dmTest.Rd man/dm_plotDataDSInfo.Rd man/dm_plotProportions.Rd man/plotData.Rd man/plotPValues.Rd man/plotPrecision.Rd man/plotProportions.Rd
tests
tests/testthat
tests/testthat.R tests/testthat/test_MatrixList.R tests/testthat/test_dm_adjustment.R tests/testthat/test_lik_score.R
vignettes
vignettes/DRIMSeq.Rnw
vignettes/References.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.