Files in HenrikBengtsson/aroma.cn
Copy-Number Analysis of Large Microarray Data Sets
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/covr.yaml
.gitignore
.make/Makefile
CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
Makefile
NAMESPACE
NEWS.md
R/000.R
R/006.fixVarArgs.R
R/009.setup.R
R/021.dynamic_imports.R
R/999.DEPRECATED.R
R/999.NonDocumentedObjects.R
R/999.package.R
R/AbstractCurveNormalization.R
R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R
R/C1C2.R
R/CBS.findAtomicAberrations.R
R/CartesianSnpData.R
R/CopyNumberRegions.findAtomicAberrations.R
R/MultiSourceCopyNumberNormalization.R
R/MultiSourceCopyNumberNormalization.XTRAS.R
R/NaiveFracBGenotyping.R
R/PairedPSCBS.BOOT.R
R/PairedPSCBS.CALL2.R
R/PairedPSCBS.NORM.R
R/PairedPSCBS.PLOT3.R
R/PairedPSCBS.backgroundCorrect.R
R/PairedPSCBS.findAtomicAberrations.R
R/PairedPSCBS.fitC1C2Peaks.R
R/PairedPSCBSFile.R
R/PairedPSCBSFileSet.R
R/PairedPscbsCaller.R
R/PairedPscbsModel.R
R/PeaksAndValleys.EXTS.R
R/PolarSnpData.R
R/PrincipalCurve.XTRAS.R
R/PrincipalCurveNormalization.R
R/PruneCNA.EXTS.R
R/PruneCNA.PLOT.R
R/RawAlleleBFractions.XTRAS.R
R/RawGenotypeCalls.R
R/SnpData.R
R/TotalCnBinnedSmoothing.R
R/TotalCnKernelSmoothing.R
R/TotalCnSmoothing.R
R/TotalFracBSnpData.R
R/TumorBoostNormalization.R
R/XYCurveNormalization.R
R/calculatePairedPSCNByGenotype.R
R/callXXorXY.numeric.R
R/cnr.R
R/fitLoessKD.matrix.R
R/normalizeMirroredBAFsByRegions.R
R/normalizePrincipalCurve.matrix.R
R/principal.curve.pairs2.R
R/pruneCNA.R
R/segmentByPruneCBS.R
R/testAllelicBalanceByBAFs.R
R/testEquality.R
R/utils.R
R/zzz.R
README.md
cran-comments.md
incl/999.missingdocs.txt
incl/BengtssonH_2003.bib.Rdoc
incl/PairedPscbsModel.Rex
incl/TotalCnBinnedSmoothing.Rex
incl/bootstrap.PairedPSCBS.Rex
incl/callAllelicBalanceByBAFs.PairedPSCBS.Rex
incl/callCopyNeutralRegions.PairedPSCBS.Rex
incl/cnr.Rex
incl/deShearC1C2.PairedPSCBS.Rex
incl/findAtomicAberrations.Rex
incl/normalizeBAFsByRegions.PairedPSCBS.Rex
incl/orthogonalizeC1C2.PairedPSCBS.Rex
incl/pruneCNA.Rex
inst/CITATION
inst/templates/rsp/PairedPSCBS,deShear,report.tex.rsp
inst/templates/rsp/bioinformatics-journals-abbr.bib
inst/templates/rsp/natbib.bst
inst/testScripts/devel/C1C2/21.PairedPSCBS,deShear,report.R
inst/testScripts/devel/C1C2/31.PairedPSCBS,DP,deShear.R
inst/testScripts/setup/01a.downloadAllAnnotationData.R
inst/testScripts/setup/01b.downloadAllRawDataSet.R
inst/testScripts/setup/01c.installAllPackages.R
inst/testScripts/setup/99a.cleanupRootDirectories.R
inst/testScripts/setup/spawnTests.sh
inst/testScripts/system/CondSegmentation/test20090927,TBN,plot.Rex
inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex
inst/testScripts/system/CopyNumberProfiles/20100909a,findAtomicAberrations.Rex
inst/testScripts/system/CopyNumberProfiles/20100909b,NormalContamination.Rex
inst/testScripts/system/CopyNumberProfiles/20100911a,TumorClonality.Rex
inst/testScripts/system/CopyNumberProfiles/20100911b,TumorClonality,lineage.Rex
inst/testScripts/system/CopyNumberProfiles/20100912a,SegmentationStdError.Rex
inst/testScripts/system/CopyNumberProfiles/20100912b,Saturation.Rex
inst/testScripts/system/CurveNormalization,OV/test20090715a,waves.Rex
inst/testScripts/system/MSLHN/20091218,TCGA,MSLHCN.Rex
inst/testScripts/system/MultiPlatform/test20090208,TCGA,MSCN.Rex
inst/testScripts/system/MultiPlatform/test20090209,TCGA,plot.Rex
inst/testScripts/system/MultiPlatform/test20090210,TCGA,MSCN,plot.Rex
inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,shifts.Rex
inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,wCBS.Rex
inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,weights.Rex
inst/testScripts/system/MultiPlatform/test20090720,TCGA,MSCN,tracks.Rex
inst/testScripts/system/MultiPlatform/test20100102,TCGA,MSCN,mpCBS.Rex
inst/testScripts/system/TumorBoost/test20090429a,NGC.Rex
inst/testScripts/system/TumorBoost/test20090429b,TBN.Rex
inst/testScripts/system/TumorBoost/test20090429c,TBN,plot.Rex
inst/testScripts/system/TumorBoost/test20090429d,TBN,LOH,plot.Rex
inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex
inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2,20111026.Rex
inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2.PairedPSCBS.Rex
inst/testScripts/system/chipTypes/GenomeWideSNP_6/deShearC1C2.PairedPSCBS.Rex
inst/testScripts/system/chipTypes/GenomeWideSNP_6/normalizeLoess2D.PairedPSCBS.Rex
inst/testScripts/system/chipTypes/GenomeWideSNP_6/orthogonalizeC1C2.PairedPSCBS.Rex
inst/testScripts/system/pairedPSCN/R/00.setup.R
inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R
inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R
inst/testScripts/system/pairedPSCN/R/zzz.R
inst/testScripts/system/pairedPSCN/genomicPlots.tex.rsp
inst/testScripts/system/segmentation/20091110,CBS.Rex
inst/testScripts/system/tracks/20091008,HCC1143,CRMAv2-dChip-GTC,plot.Rex
inst/testScripts/system/tracks/20091010,TCGA,plot.Rex
inst/testScripts/system/tracks/utils.R
man/AbstractCurveNormalization.Rd
man/MultiSourceCopyNumberNormalization.Rd
man/Non-documented_objects.Rd
man/PairedPscbsModel.Rd
man/PrincipalCurveNormalization.Rd
man/TotalCnBinnedSmoothing.Rd
man/TotalCnKernelSmoothing.Rd
man/TotalCnSmoothing.Rd
man/TumorBoostNormalization.Rd
man/XYCurveNormalization.Rd
man/aroma.cn-package.Rd
man/callAllelicBalanceByBAFs.PairedPSCBS.Rd
man/callCopyNeutralRegions.PairedPSCBS.Rd
man/callPeaks.PeaksAndValleys.Rd
man/callXXorXY.numeric.Rd
man/cnr.Rd
man/extractTupleOfDataFiles.MultiSourceCopyNumberNormalization.Rd
man/findAtomicAberrations.CopyNumberRegions.Rd
man/fitOne.MultiSourceCopyNumberNormalization.Rd
man/getAllNames.MultiSourceCopyNumberNormalization.Rd
man/getFitAromaUgpFile.MultiSourceCopyNumberNormalization.Rd
man/getInputDataSets.MultiSourceCopyNumberNormalization.Rd
man/getSmoothedDataSets.MultiSourceCopyNumberNormalization.Rd
man/getSubsetToFit.MultiSourceCopyNumberNormalization.Rd
man/normalizeBAFsByRegions.PairedPSCBS.Rd
man/normalizeMirroredBAFsByRegions.matrix.Rd
man/normalizePrincipalCurve.matrix.Rd
man/process.MultiSourceCopyNumberNormalization.Rd
man/testAllelicBalanceByBAFs.Rd
revdep/README.md
revdep/cran.md
revdep/failures.md
revdep/problems.md
revdep/run.R
tests/callAllelicBalanceByBAFs.PairedPSCBS.R
tests/cnr.R
