Files in haibol2016/InPAS
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
.Rbuildignore
.gitignore
DESCRIPTION
InPAS-master.Rproj
NAMESPACE
NEWS
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
data/datalist
data/utr3.mm10.rda
inst/extdata/Baf3.extract.bedgraph
inst/extdata/UM15.extract.bedgraph
inst/extdata/eset.MAQC.rda
inst/extdata/polyA.rda
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
vignettes/nature.csl
vignettes/ref.bib
