Files in HenrikBengtsson/aroma.tcga
Methods for accessing online The Cancer Genome Atlas (TCGA) data
DESCRIPTION
R/000.R
R/006.fixVarArgs.R
R/999.NonDocumentedObjects.R
R/999.package.R
R/BiospecimenCoreResource.R
R/BroadAfter5NNTotalCopyNumberTcgaDataFile.R
R/BroadAfter5NNTotalCopyNumberTcgaDataFileSet.R
R/BroadAlleleSpecificCopyNumberTcgaDataFile.R
R/BroadAlleleSpecificCopyNumberTcgaDataFileSet.R
R/BroadAlleleSpecificThetaTcgaDataFile.R
R/BroadAlleleSpecificThetaTcgaDataFileSet.R
R/BroadBirdseedGenotypeTcgaDataFile.R
R/BroadBirdseedGenotypeTcgaDataFile.exportGenotypeCallsAndConfidenceScores.R
R/BroadBirdseedGenotypeTcgaDataFileSet.R
R/BroadTotalCopyNumberTcgaDataFile.R
R/BroadTotalCopyNumberTcgaDataFile.exportTotalAndFracB.R
R/BroadTotalCopyNumberTcgaDataFileSet.R
R/BroadTotalCopyNumberTcgaDataFileSet.exportTotalAndFracB.R
R/GenericDataFileSet.XTRAS.R
R/HarvardTotalCopyNumberTcgaDataFile.R
R/HarvardTotalCopyNumberTcgaDataFileSet.R
R/HudsonAlphaBAlleleFreqTcgaDataFile.R
R/HudsonAlphaBAlleleFreqTcgaDataFileSet.R
R/HudsonAlphaGenotypeTcgaDataFile.R
R/HudsonAlphaGenotypeTcgaDataFile.exportGenotypeCalls.R
R/HudsonAlphaGenotypeTcgaDataFileSet.R
R/HudsonAlphaXYTcgaDataFile.R
R/HudsonAlphaXYTcgaDataFileSet.R
R/MageTabDataMatrixFile.R
R/MageTabDataMatrixFileSet.R
R/MageTabFile.R
R/MageTabFileSet.R
R/MscnExport.R
R/MskccTotalCopyNumberTcgaDataFile.R
R/MskccTotalCopyNumberTcgaDataFileSet.R
R/MultisourceChromosomalModel.R
R/MultisourceCopyNumberChromosomalModel.R
R/RawMultisourceCopyNumberModel.R
R/SdrfFile.R
R/SdrfFileSet.R
R/TcgaDataFile.R
R/TcgaDataFileSet.R
R/TcgaDccData.R
R/TcgaDccData.findDataSets.R
R/TcgaDccDownloader.R
R/TcgaDccDownloader.readBCRSamplesTable.R
R/TcgaFullNameTranslators.R
R/parseSdrfExtractName.R
R/parseTcgaDccArchiveName.R
R/pruneSDRF.R
R/readSDRFFile.R
R/readSDRFFolder.R
R/tcgaDccFullnameTranslator.R
R/zzz.R
incl/999.missingdocs.txt
inst/NEWS
inst/testScripts/system/A1.download/1.buildDirectoryStubs.Rex
inst/testScripts/system/A1.download/2.download.Rex
inst/testScripts/system/A1.download/3.downloadBCRTable.Rex
inst/testScripts/system/A1.download/TCGA,DCC,dirs,GBM.txt
inst/testScripts/system/A1.download/TCGA,DCC,dirs,OV.txt
inst/testScripts/system/A2.createLinks/1.LinkRawDataToTCGAData.Rex
inst/testScripts/system/A3.import/1.import.Rex
inst/testScripts/system/A4.CRMAv2/1.ASCRMAv2.Rex
inst/testScripts/system/A4.CRMAv2/3.import.Rex
inst/testScripts/system/B1.normalize/1.PrincipalCurveNormalization.Rex
inst/testScripts/system/B1.ratios/1.CalculateTumorNormalCnRatios.Rex
inst/testScripts/system/B2.QC/1.PairedTumorNormalBAFs.Rex
inst/testScripts/system/D1.scan/1.msTabulate.Rex
inst/testScripts/system/D2.MSCN/1.MSCN,batch.Rex
inst/testScripts/system/D2.MSCN/1.MSCN,presmooting.Rex
inst/testScripts/system/D2.MSCN/2.MSCN,subset.Rex
inst/testScripts/system/D4.QC/1.MSCN,QC,tracks.Rex
inst/testScripts/system/D9.export/1.export.Rex
inst/testScripts/system/E1.segmentation/1.CBS,subset.Rex
inst/testScripts/system/qc/test20090930,MSCN,QC,tracks.Rex
inst/testScripts/system/scan/test20090929,findSamples.Rex
man/MultisourceChromosomalModel.Rd
man/MultisourceCopyNumberChromosomalModel.Rd
man/Non-documented_objects.Rd
man/RawMultisourceCopyNumberModel.Rd
man/aroma.tcga-package.Rd
man/exportGenotypeCalls.HudsonAlphaGenotypeTcgaDataFile.Rd
man/exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFile.Rd
man/fit.MultisourceCopyNumberChromosomalModel.Rd
man/getChromosomes.MultisourceChromosomalModel.Rd
man/getNames.MultisourceChromosomalModel.Rd
man/nbrOfArrays.MultisourceChromosomalModel.Rd
man/parseTcgaDccArchiveName.character.Rd
man/tcgaDccFullnameTranslator.character.Rd
