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.

Author
Malgorzata Nowicka [aut, cre]
Date of publication
None
Maintainer
Malgorzata Nowicka <gosia.nowicka@uzh.ch>
License
GPL (>= 3)
Version
1.2.0

View on Bioconductor

Man pages

data_dmDSdata
Sample data for differential splicing analysis
data_dmSQTLdata
Sample data for sQTL analysis
dmDispersion
Estimate dispersions in Dirichlet-multinomial model
dmDSdata
Create dmDSdata object Constructor function for a 'dmDSdata'...
dmDSdata-class
dmDSdata object
dmDSdispersion-class
dmDSdispersion object
dmDSfit-class
dmDSfit object
dmDStest-class
dmDStest object
dmFilter
Filtering
dmFit
Estimate proportions in Dirichlet-multinomial model
dm_plotDataDSInfo
Plot the frequency of present features
dm_plotProportions
Plot feature proportions
dmSQTLdata
Create dmSQTLdata object
dmSQTLdata-class
dmSQTLdata object
dmSQTLdispersion-class
dmSQTLdispersion object
dmSQTLfit-class
dmSQTLfit object
dmSQTLtest-class
dmSQTLtest object
dmTest
Likelihood ratio test
MatrixList-class
MatrixList object
plotData
Plot data summary
plotDispersion
Dispersion versus mean expression plot
plotFit
Plot feature proportions
plotTest
Plot p-values distribution

Files in this package

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