R Packages that start with:
A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .
Functions
- AddAndCheckDBSClassInVCF()
- AddAndCheckSBSClassInVCF()
- AddDBSClass()
- AddRunInformation()
- AddSBSClass()
- AddSeqContext()
- AddTranscript()
- all.abundance()
- AnnotateDBSVCF()
- AnnotateIDVCF()
- AnnotateSBSVCF()
- as.catalog()
- CalBaseCountsFrom3MerAbundance()
- CalculateNumberOfSpace()
- Canonicalize1Del()
- Canonicalize1ID()
- Canonicalize1INS()
- CanonicalizeID()
- CatalogRowOrder()
- CheckAndFixChrNames()
- CheckAndFixChrNamesForTransRanges()
- CheckAndReorderRownames()
- CheckAndReturnDBSCatalogs()
- CheckAndReturnDBSMatrix()
- CheckAndReturnIDCatalog()
- CheckAndReturnIDMatrix()
- CheckAndReturnSBSCatalogs()
- CheckAndReturnSBSMatrix()
- CheckDBSClassInVCF()
- CheckSBSClassInVCF()
- CheckSeqContextInVCF()
- CollapseCatalog()
- ConvertICAMSCatalogToSigProSBS96()
- CreateDinucAbundance()
- CreateExomeStrandedRanges()
- CreateOneColDBSMatrix()
- CreateOneColIDMatrix()
- CreateOneColSBSMatrix()
- CreateOnePPMFromSBSVCF()
- CreatePentanucAbundance()
- CreatePPMFromSBSVCFs()
- CreateStrandedDinucAbundance()
- CreateStrandedTrinucAbundance()
- CreateTetranucAbundance()
- CreateTransRanges()
- CreateTrinucAbundance()
- FindDelMH()
- FindMaxRepeatDel()
- FindMaxRepeatIns()
- GeneExpressionData()
- GenerateEmptyKmerCounts()
- GenerateKmer()
- GetConsensusVAF()
- GetCustomKmerCounts()
- GetGenomeKmerCounts()
- GetMutationLoadsFromMutectVCFs()
- GetMutationLoadsFromStrelkaIDVCFs()
- GetMutationLoadsFromStrelkaSBSVCFs()
- GetSequenceKmerCounts()
- GetStrandedKmerCounts()
- GetVAF()
- ICAMS()
- InferAbundance()
- InferCatalogClassPrefix()
- InferCatalogInfo()
- InferRownames()
- IsGRCh37()
- IsGRCh38()
- IsGRCm38()
- MakeDataFrameFromVCF()
- MakeVCFDBSdf()
- MutectVCFFilesToCatalog()
- MutectVCFFilesToCatalogAndPlotToPdf()
- MutectVCFFilesToZipFile()
- NormalizeGenomeArg()
- Plot96PartOfCompositeToPDF()
- PlotCatalog()
- PlotCatalogToPdf()
- PlotPPM()
- PlotPPMToPdf()
- PlotTransBiasGeneExp()
- PlotTransBiasGeneExpToPdf()
- ReadAndSplitMutectVCFs()
- ReadAndSplitStrelkaSBSVCFs()
- ReadAndSplitVCFs()
- ReadBedRanges()
- ReadCatalog()
- ReadCatalogErrReturn()
- ReadCatalogInternal()
- ReadDukeNUSCat192()
- ReadMutectVCF()
- ReadMutectVCFs()
- ReadStapleGT96SBS()
- ReadStrelkaIDVCF()
- ReadStrelkaIDVCFs()
- ReadStrelkaSBSVCF()
- ReadStrelkaSBSVCFs()
- ReadTranscriptRanges()
- ReadVCF()
- ReadVCFs()
- RemoveRangesOnBothStrand()
- RenameColumnsWithNameStrand()
- RenameColumnsWithNameVAF()
- Restaple96()
- Restaple1536()
- revc()
- RevcDBS144()
- RevcSBS96()
- SplitListOfMutectVCFs()
- SplitListOfStrelkaSBSVCFs()
- SplitListOfVCFs()
- SplitOneMutectVCF()
- SplitOneVCF()
- SplitSBSVCF()
- SplitStrelkaSBSVCF()
- StandardChromName()
- StandardChromNameNew()
- StopIfCatalogTypeIllegal()
- StopIfNrowIllegal()
- StopIfRegionIllegal()
- StopIfTranscribedRegionIllegal()
- StrelkaIDVCFFilesToCatalog()
- StrelkaIDVCFFilesToCatalogAndPlotToPdf()
- StrelkaIDVCFFilesToZipFile()
- StrelkaSBSVCFFilesToCatalog()
- StrelkaSBSVCFFilesToCatalogAndPlotToPdf()
- StrelkaSBSVCFFilesToZipFile()
- TCFromCouSigCou()
- TCFromDenSigDen()
- TestMakeCatalogFromMutectVCFs()
- TestMakeCatalogFromStrelkaIDVCFs()
- TestMakeCatalogFromStrelkaSBSVCFs()
- TestPlotCatCOMPOSITE()
- TranscriptRanges()
- TransformCatalog()
- TransRownames.ID.PCAWG.SigPro()
- TransRownames.ID.SigPro.PCAWG()
- Unstaple78()
- Unstaple96()
- Unstaple1536()
- VCFsToCatalogs()
- VCFsToCatalogsAndPlotToPdf()
- VCFsToDBSCatalogs()
- VCFsToIDCatalogs()
- VCFsToSBSCatalogs()
- VCFsToZipFile()
- VCFsToZipFileXtra()
- WriteCat()
- WriteCatalog()
- WriteCatalogIndelSigPro()
R Codes
Selected R package: ICAMS
Click on the specific functions, references or examples using the links on the left
This will display the example document in this panel! Call for submissions of examples for R packages. Contribute today!