Files in InPAS

InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

README.md R/testUsage.R R/utr3Annotation.R R/depthWeight.R R/covThreshold.R R/seqLen.R R/searchProximalCPs.R R/fisher.exact.test.R R/get.regions.coverage.R R/proximalAdjByPWM.R R/mergeCoverage.R R/zScoreThrethold.R R/UTR3usage.R R/searchDistalCPs.R R/Comp.R R/sortGR.R R/singleGroupAnalyze.R R/optimalSegmentation.R R/usage4plot.R R/coverageRate.R R/filterRes.R R/lastCDSusage.R R/PAscore2.R R/getUTR3eSet.R R/removeUTR3__UTR3.R R/valley.R R/getCov.R R/limmaAnalyze.R R/PAscore.R R/proximalAdj.R R/CPsite_estimation.R R/distalAdj.R R/UTR3TotalCoverage.R R/polishCPs.R R/getUTR3region.R R/inPAS.R R/CPsites.R R/singleSampleAnalyze.R R/utr3UsageEstimation.R R/coverageFromBedGraph.R R/totalCoverage.R R/UTR3eSet.R R/trimSeqnames.R R/prepare4GSEA.R R/proximalAdjByCleanUpdTSeq.R vignettes/InPAS.Rmd man/totalCoverage.Rd man/getUTR3eSet.Rd man/lastCDSusage.Rd man/usage4plot.Rd man/polishCPs.Rd man/utr3Annotation.Rd man/get.regions.coverage.Rd man/PAscore2.Rd man/CPsites.Rd man/covThreshold.Rd man/fisher.exact.test.Rd man/filterRes.Rd man/utr3.danRer10.Rd man/removeUTR3__UTR3.Rd man/utr3.mm10.Rd man/searchDistalCPs.Rd man/singleGroupAnalyze.Rd man/UTR3usage.Rd man/zScoreThrethold.Rd man/InPAS-package.Rd man/singleSampleAnalyze.Rd man/valley.Rd man/utr3.hg19.Rd man/prepare4GSEA.Rd man/seqLen.Rd man/CPsite_estimation.Rd man/inPAS.Rd man/UTR3TotalCoverage.Rd man/getUTR3region.Rd man/optimalSegmentation.Rd man/PAscore.Rd man/trimSeqnames.Rd man/depthWeight.Rd man/coverageFromBedGraph.Rd man/distalAdj.Rd man/proximalAdjByCleanUpdTSeq.Rd man/coverageRate.Rd man/limmaAnalyze.Rd man/utr3UsageEstimation.Rd man/proximalAdj.Rd man/sortGR.Rd man/testUsage.Rd man/proximalAdjByPWM.Rd man/searchProximalCPs.Rd man/UTR3eSet.Rd man/getCov.Rd tests/runTests.R inst/doc/InPAS.Rmd inst/doc/InPAS.R inst/unitTests/test_getUTR3eSet.R inst/unitTests/test_CPsites.R inst/unitTests/test_coverageFromBedGraph.R