Files in haibol2016/InPAS

Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

R/00.InPAS-package.R R/00.data.R R/00.get_GCandMappability.R R/00.get_lastCDSUTR3.R R/00.get_seqLen.R R/00.set_globals.R R/00.setup_sqlitedb.R R/00.trim_seqnames.R R/01.parse_TxDb.R R/02.extract_UTR3Anno.R R/03.get_ssRleCov.R R/04.get_chromosomes.R R/05.assemble_allCov.R R/06.run_coverageQC.R R/07.get_depthWeight.R R/08.get_totalCov.R R/09.get_zScoreCutoff.R R/10.get_UTR3TotalCov.R R/11.setup_CPsSearch.R R/12.search_CPs.R R/13.search_distalCPs.R R/14.adjust_distalCPs.R R/14.get_PAscore2.R R/14.remove_convergentUTR3s.R R/15.adjust_proximalCPs.R R/15.adjust_proximalCPsByNBC.R R/15.adjust_proximalCPsByPWM.R R/15.calculate_mse.R R/15.find_valleyBySpline.R R/15.get_PAscore.R R/15.search_proximalCPs.R R/16.find_minMSEDistr.R R/17.polish_CPs.R R/18.get_UTR3CDS.R R/18.get_UTR3region.R R/19.get_regionCov.R R/20.UTR3eSet-class.R R/21.get_UTR3eSet.R R/22.test_dPDUI.R R/23.run_fisherExactTest.R R/23.run_limmaAnalysis.R R/23.run_singleGroupAnalysis.R R/23.run_singleSampleAnalysis.R R/24.filter_testOut.R R/25.setup_GSEA.R R/26.get_usage4plot.R R/27.plot_utr3Usage.R README.md inst/unitTests/test_get_ssRleCov.R inst/unitTests/test_search_CPs.R man/InPAS.Rd man/UTR3eSet-class.Rd man/addChr2Exclude.Rd man/addInPASEnsDb.Rd man/addInPASGenome.Rd man/addInPASOutputDirectory.Rd man/addInPASTxDb.Rd man/addLockName.Rd man/adjust_distalCPs.Rd man/adjust_proximalCPs.Rd man/adjust_proximalCPsByNBC.Rd man/adjust_proximalCPsByPWM.Rd man/assemble_allCov.Rd man/assign_feature.Rd man/calculate_mse.Rd man/compensation.Rd man/dot-onAttach.Rd man/extract_UTR3Anno.Rd man/fft.smooth.Rd man/filter_testOut.Rd man/find_minMSEDistr.Rd man/find_valleyBySpline.Rd man/gcComp.Rd man/gcContents.Rd man/getChr2Exclude.Rd man/getInPASEnsDb.Rd man/getInPASGenome.Rd man/getInPASOutputDirectory.Rd man/getInPASSQLiteDb.Rd man/getInPASTxDb.Rd man/getLockName.Rd man/get_PAscore.Rd man/get_PAscore2.Rd man/get_UTR3CDS.Rd man/get_UTR3TotalCov.Rd man/get_UTR3eSet.Rd man/get_UTR3region.Rd man/get_chromosomes.Rd man/get_depthWeight.Rd man/get_lastCDSUTR3.Rd man/get_regionCov.Rd man/get_seqLen.Rd man/get_ssRleCov.Rd man/get_totalCov.Rd man/get_usage4plot.Rd man/get_zScoreCutoff.Rd man/mapComp.Rd man/parse_TxDb.Rd man/plot_utr3Usage.Rd man/polish_CPs.Rd man/remove_convergentUTR3s.Rd man/run_coverageQC.Rd man/run_fisherExactTest.Rd man/run_limmaAnalysis.Rd man/run_singleGroupAnalysis.Rd man/run_singleSampleAnalysis.Rd man/search_CPs.Rd man/search_distalCPs.Rd man/search_proximalCPs.Rd man/set_globals.Rd man/setup_CPsSearch.Rd man/setup_GSEA.Rd man/setup_parCPsSearch.Rd man/setup_sqlitedb.Rd man/test_dPDUI.Rd man/trim_seqnames.Rd man/utr3.mm10.Rd tests/runTests.R vignettes/InPAS.Rmd