Files in HenrikBengtsson/PSCBS
Analysis of Parent-Specific DNA Copy Numbers

.Rbuildignore

.Rinstignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.github/workflows/revdepcheck-top.yaml

.github/workflows/test-coverage.yaml

.gitignore

.make/Makefile

CONDUCT.md CONTRIBUTING.md

DESCRIPTION

Makefile

NAMESPACE

NEWS.md R/000.R R/999.NonDocumentedObjects.R R/999.package.R R/AbstractCBS.HCLUST.R R/AbstractCBS.PLOT.R R/AbstractCBS.PRUNE.R R/AbstractCBS.R R/AbstractCBS.REPORT.R R/AbstractCBS.RESTRUCT.R R/AbstractCBS.clearCalls.R R/CBS.CALL.R R/CBS.EXTS.R R/CBS.IO.R R/CBS.PLOT,many.R R/CBS.PLOT.R R/CBS.PRUNE.R R/CBS.R R/CBS.RESTRUCT.R R/CBS.SMOOTH.R R/CBS.joinSegments.R R/CBS.updateMeansTogether.R R/CNA.EXTS.R R/DNAcopy.EXTS.R R/NonPairedPSCBS.R R/PSCBS.IO.R R/PSCBS.R R/PSCBS.RESTRUCT.R R/PSCBS.isLocallyPhased.R R/PairedPSCBS.BOOT.R R/PairedPSCBS.BOOT.sets.R R/PairedPSCBS.CALL.R R/PairedPSCBS.EXTS.R R/PairedPSCBS.EXTS3.R R/PairedPSCBS.PLOT,many.R R/PairedPSCBS.PLOT.R R/PairedPSCBS.PLOT2.R R/PairedPSCBS.PRUNE.R R/PairedPSCBS.R R/PairedPSCBS.RESTRUCT.R R/PairedPSCBS.applyByRegion.R R/PairedPSCBS.callAB.R R/PairedPSCBS.callCopyNeutral.R R/PairedPSCBS.callGNL.R R/PairedPSCBS.callLOH.R R/PairedPSCBS.callROH.R R/PairedPSCBS.estimateDeltaAB.R R/PairedPSCBS.estimateDeltaLOH.R R/PairedPSCBS.estimateKappa.R R/PairedPSCBS.extractSegmentDataByLocus.R R/PairedPSCBS.unTumorBoost.R R/PairedPSCBS.updateMeans.R R/PairedPSCBS.updateMeansTogether.R R/callSegmentationOutliers.R R/drawLevels.DNAcopy.R R/exampleData.R R/findLargeGaps.R R/findNeutralCopyNumberState.R R/gapsToSegments.R R/installDNAcopy.R R/prememoize.R R/randomSeed.R R/segmentByCBS.R R/segmentByNonPairedPSCBS.R R/segmentByPairedPSCBS.R R/testROH.R R/utils.R R/weightedQuantile.R R/writeWIG.R R/zzz.R README.md

incl/999.missingdocs.txt

incl/BengtssonH_etal_2010.Rd

incl/INSTALL.md incl/OVERVIEW.md

incl/OlshenA_etal_2011.Rd

incl/OlshenVenkatraman_2004.Rd

incl/VenkatramanOlshen_2007.Rd

incl/as.DNAcopy.Rex

incl/segmentByCBS,calls.Rex

incl/segmentByCBS,knownSegments.Rex

incl/segmentByCBS,plot.Rex

incl/segmentByCBS,pruneBySdUndo.Rex

incl/segmentByCBS,tests.Rex

incl/segmentByCBS.Rex

incl/segmentByNonPairedPSCBS.Rex

incl/segmentByPairedPSCBS,HetsAndHoms.Rex

incl/segmentByPairedPSCBS,allLOH.Rex

incl/segmentByPairedPSCBS.Rex

inst/CITATION

inst/WORDLIST

inst/data-ex/PairedPSCBS,exData,chr01.Rbin

inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/0109d43cd74c8e7e46db1abde235c808.Rcache

inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/2aba5b85ae757609b8b4c9fc60be1156.Rcache

inst/templates/rsp/CBS,report.tex.rsp

inst/templates/rsp/NonPairedPSCBS,report.tex.rsp

inst/templates/rsp/PSCBS.bib

inst/templates/rsp/PairedPSCBS,report.tex.rsp

inst/templates/rsp/bioinformatics-journals-abbr.bib

inst/templates/rsp/includes/levelDensities.tex.rsp

inst/templates/rsp/includes/pscnSegmentationTracks.tex.rsp

inst/templates/rsp/includes/pscnSegmentationTransitions.tex.rsp

inst/templates/rsp/includes/references.tex.rsp

inst/templates/rsp/includes/reportHeader.tex.rsp

inst/templates/rsp/includes/reportSetupGraphics.tex.rsp

inst/templates/rsp/includes/reportSetupMacros.tex.rsp

inst/templates/rsp/includes/sessionInfo.tex.rsp

inst/templates/rsp/includes/signalDensities.tex.rsp

inst/templates/rsp/includes/summaryOfAnnotationAndGenotypeCalls.tex.rsp

inst/templates/rsp/natbib.bst

man/figures/ex-PSCBS-paired.chr01.png

vignettes/CBS.tex.rsp

vignettes/PSCBS.bib

vignettes/PairedPSCBS.tex.rsp

vignettes/natbib.bst

HenrikBengtsson/PSCBS documentation built on June 8, 2025, 10:40 p.m.

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HenrikBengtsson/PSCBS
Analysis of Parent-Specific DNA Copy Numbers

Files in HenrikBengtsson/PSCBS
Analysis of Parent-Specific DNA Copy Numbers

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HenrikBengtsson/PSCBS Analysis of Parent-Specific DNA Copy Numbers

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HenrikBengtsson/PSCBS
Analysis of Parent-Specific DNA Copy Numbers

Files in HenrikBengtsson/PSCBS
Analysis of Parent-Specific DNA Copy Numbers