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

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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

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