DRIMSeq: Differential splicing and sQTL analyses with Dirichlet-multinomial model in RNA-Seq

The package provides two frameworks. One for the differential splicing analysis between different conditions and one for the sQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts, exons or exonic bins) with Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.

AuthorMalgorzata Nowicka [aut, cre]
Date of publicationNone
MaintainerMalgorzata Nowicka <gosia.nowicka@uzh.ch>
LicenseGPL (>= 3)
Version1.2.0

View on Bioconductor

Functions

colnames<-,MatrixList-method Man page
colnames,MatrixList-method Man page
common_dispersion Man page
common_dispersion<- Man page
common_dispersion<-,dmDSdispersion-method Man page
common_dispersion,dmDSdispersion-method Man page
counts,dmDSdata-method Man page
data_dmDSdata Man page
data_dmSQTLdata Man page
dim,MatrixList-method Man page
dm_counts Man page
dm_counts,dmDSdata-method Man page
dmDispersion Man page
dmDispersion,dmDSdata-method Man page
dmDispersion,dmSQTLdata-method Man page
dmDSdata Man page
[,dmDSdata,ANY-method Man page
dmDSdata-class Man page
[,dmDSdata-method Man page
dmDSdispersion-class Man page
dmDSfit-class Man page
dmDStest-class Man page
dmFilter Man page
dmFilter,dmDSdata-method Man page
dmFilter,dmSQTLdata-method Man page
dmFit Man page
dmFit,dmDSdispersion-method Man page
dmFit,dmSQTLdispersion-method Man page
dm_plotDataDSInfo Man page
dm_plotProportions Man page
dm_samples Man page
dm_samples,dmDSdata-method Man page
dmSQTLdata Man page
[,dmSQTLdata,ANY-method Man page
dmSQTLdata-class Man page
dmSQTLdataFromRanges Man page
[,dmSQTLdata-method Man page
dmSQTLdispersion-class Man page
dmSQTLfit-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_dispersion Man page
genewise_dispersion<- Man page
genewise_dispersion<-,dmDSdispersion-method Man page
genewise_dispersion,dmDSdispersion-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,dmDSdispersion-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
plotDispersion Man page
plotDispersion,dmDSdispersion-method Man page
plotDispersion,dmSQTLdispersion-method Man page
plotFit Man page
plotFit,dmDSfit-method Man page
plotFit,dmDStest-method Man page
plotFit,dmSQTLfit-method Man page
plotFit,dmSQTLtest-method Man page
plotTest Man page
plotTest,dmDStest-method Man page
plotTest,dmSQTLtest-method Man page
proportions Man page
proportions,dmDSfit-method Man page
proportions,dmDStest-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
statistics Man page
statistics,dmDSfit-method Man page
statistics,dmDStest-method Man page

Files

DRIMSeq/DESCRIPTION
DRIMSeq/NAMESPACE
DRIMSeq/NEWS
DRIMSeq/R
DRIMSeq/R/DRIMSeq.R DRIMSeq/R/class_MatrixList.R DRIMSeq/R/class_dmDSdata.R DRIMSeq/R/class_dmDSdispersion.R DRIMSeq/R/class_dmDSfit.R DRIMSeq/R/class_dmDStest.R DRIMSeq/R/class_dmSQTLdata.R DRIMSeq/R/class_dmSQTLdispersion.R DRIMSeq/R/class_dmSQTLfit.R DRIMSeq/R/class_dmSQTLtest.R DRIMSeq/R/class_show_utils.R DRIMSeq/R/dmDS_adjustmentCommon.R DRIMSeq/R/dmDS_estimateCommonDispersion.R DRIMSeq/R/dmDS_estimateTagwiseDispersion.R DRIMSeq/R/dmDS_filter.R DRIMSeq/R/dmDS_fitOneModel.R DRIMSeq/R/dmDS_plotFit.R DRIMSeq/R/dmDS_profileLikCommon.R DRIMSeq/R/dmDS_test.R DRIMSeq/R/dmSQTL_adjustmentCommon.R DRIMSeq/R/dmSQTL_estimateCommonDispersion.R DRIMSeq/R/dmSQTL_estimateTagwiseDispersion.R DRIMSeq/R/dmSQTL_filter.R DRIMSeq/R/dmSQTL_fitOneModel.R DRIMSeq/R/dmSQTL_plotFit.R DRIMSeq/R/dmSQTL_profileLikCommon.R DRIMSeq/R/dmSQTL_test.R DRIMSeq/R/dm_Hessian.R DRIMSeq/R/dm_NewtonRaphson.R DRIMSeq/R/dm_adjustmentOneGeneManyGroups.R DRIMSeq/R/dm_adjustmentOneGeneOneGroup.R DRIMSeq/R/dm_colorb.R DRIMSeq/R/dm_deviance.R DRIMSeq/R/dm_estimateMeanExpression.R DRIMSeq/R/dm_fitOneGeneManyGroups.R DRIMSeq/R/dm_fitOneGeneOneGroup.R DRIMSeq/R/dm_lik.R DRIMSeq/R/dm_plotData.R DRIMSeq/R/dm_plotDispersion.R DRIMSeq/R/dm_plotProportions.R DRIMSeq/R/dm_plotPvalues.R DRIMSeq/R/dm_profileLikTagwise.R DRIMSeq/R/dm_rdirichlet.R DRIMSeq/R/dm_score.R DRIMSeq/R/dm_weirMoM.R
DRIMSeq/README.md
DRIMSeq/build
DRIMSeq/build/vignette.rds
DRIMSeq/data
DRIMSeq/data/data_dmDSdata.rda
DRIMSeq/data/data_dmSQTLdata.rda
DRIMSeq/inst
DRIMSeq/inst/doc
DRIMSeq/inst/doc/DRIMSeq.R
DRIMSeq/inst/doc/DRIMSeq.Rnw
DRIMSeq/inst/doc/DRIMSeq.pdf
DRIMSeq/man
DRIMSeq/man/MatrixList-class.Rd DRIMSeq/man/data_dmDSdata.Rd DRIMSeq/man/data_dmSQTLdata.Rd DRIMSeq/man/dmDSdata-class.Rd DRIMSeq/man/dmDSdata.Rd DRIMSeq/man/dmDSdispersion-class.Rd DRIMSeq/man/dmDSfit-class.Rd DRIMSeq/man/dmDStest-class.Rd DRIMSeq/man/dmDispersion.Rd DRIMSeq/man/dmFilter.Rd DRIMSeq/man/dmFit.Rd DRIMSeq/man/dmSQTLdata-class.Rd DRIMSeq/man/dmSQTLdata.Rd DRIMSeq/man/dmSQTLdispersion-class.Rd DRIMSeq/man/dmSQTLfit-class.Rd DRIMSeq/man/dmSQTLtest-class.Rd DRIMSeq/man/dmTest.Rd DRIMSeq/man/dm_plotDataDSInfo.Rd DRIMSeq/man/dm_plotProportions.Rd DRIMSeq/man/plotData.Rd DRIMSeq/man/plotDispersion.Rd DRIMSeq/man/plotFit.Rd DRIMSeq/man/plotTest.Rd
DRIMSeq/tests
DRIMSeq/tests/testthat
DRIMSeq/tests/testthat.R
DRIMSeq/tests/testthat/test_MatrixList.R
DRIMSeq/tests/testthat/test_dm_adjustment.R
DRIMSeq/tests/testthat/test_dm_fit.R
DRIMSeq/tests/testthat/test_lik_score.R
DRIMSeq/vignettes
DRIMSeq/vignettes/DRIMSeq.Rnw
DRIMSeq/vignettes/DRIMSeq.bib

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