ICAMS
In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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Files in ICAMS
In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

MD5
NEWS.md README.md
NAMESPACE
DESCRIPTION
LICENSE
R/sysdata.rda
R/read_write_catalog.R R/shiny_related_functions.R R/other_catalog_formats.R R/data.R R/COMPOSITE.R R/chromosome_name_functions.R R/ID_functions.R R/plot.R R/sequence_context_functions.R R/utility_functions.R R/ICAMS.R R/test_functions.R R/VCF_to_catalog_functions.R R/strandbias_functions.R R/infer_catalog_format.R
inst/CITATION
inst/WORDLIST
inst/extdata/strelka.regress.cat.dbs.144.csv
inst/extdata/mutect.regress.cat.dbs.144.csv
inst/extdata/strelka.regress.cat.sbs.192.csv
inst/extdata/mutect.regress.cat.indels.csv
inst/extdata/mutect.regress.cat.dbs.136.csv
inst/extdata/strelka.regress.cat.dbs.78.csv
inst/extdata/strelka.regress.cat.sbs.1536.csv
inst/extdata/mutect.regress.cat.sbs.1536.csv
inst/extdata/strelka.regress.cat.dbs.136.csv
inst/extdata/mutect.regress.cat.dbs.78.csv
inst/extdata/strelka.regress.cat.indels.csv
inst/extdata/mutect.regress.cat.sbs.192.csv
inst/extdata/mutect.regress.cat.sbs.96.csv
inst/extdata/strelka.regress.cat.sbs.96.csv
inst/extdata/Strelka-ID-vcf/Strelka.ID.GRCh37.s1.vcf
inst/extdata/Strelka-ID-vcf/Strelka.ID.GRCh37.s2.vcf
inst/extdata/Strelka-SBS-vcf/Strelka.SBS.GRCh37.s2.vcf
inst/extdata/Strelka-SBS-vcf/Strelka.SBS.GRCh37.s1.vcf
inst/extdata/Mutect-vcf/Mutect.GRCh37.s2.vcf
inst/extdata/Mutect-vcf/Mutect.GRCh37.s1.vcf
tests/testthat.R tests/testthat/test_1strandbias_functions.R tests/testthat/test_PlotCatalogToPdf.SBS192Catalog.R tests/testthat/test_SigProfiler_formats.R tests/testthat/test_0TransformCatalogDBS144.R tests/testthat/test_COMPOSITE.R tests/testthat/test_PlotCatalog.SBS192Catalog.R tests/testthat/test_discarded_variants.R tests/testthat/test_PlotCatalogToPdf.SBS1536Catalog.R tests/testthat/test_AnnotateIDVCF.R tests/testthat/test_PlotCatalog.DBS136Catalog.R tests/testthat/test_PlotCatalog.DBS78Catalog.R tests/testthat/test_COSMIC_signature_identity.R tests/testthat/test_ReadStrelkaSBSVCF.R tests/testthat/test_RevcDBS144.R tests/testthat/test_extended_seq.context_functions.R tests/testthat/test_VCF_variant_caller_unknown.R tests/testthat/test_CanonicalizeDBS.R tests/testthat/test_1TransformCatalog.R tests/testthat/test_PlotCatalog.SBS1536Catalog.R tests/testthat/test_PlotCatalog_for_matrix_like_object.R tests/testthat/test_PlotCatalog.DBS144Catalog.R tests/testthat/test_as.catalog.R tests/testthat/test_VCFsToCatalogs.R tests/testthat/test_parallel_computing.R tests/testthat/test_0TransformCatalogSBS192.R tests/testthat/test_PlotCatalogToPdf.DBS78Catalog.R tests/testthat/test_ReadCatalog.R tests/testthat/test_PlotCatalogToPdf_for_matrix_like_object.R tests/testthat/test_PlotCatalogToPdf.DBS144Catalog.R tests/testthat/test_MakeCatalogFromStrelkaGRCh38VCF.R tests/testthat/test_PlotCatalogToPdf.IndelCatalog.R tests/testthat/test_CollapseCatalog.R tests/testthat/test_SplitStrelkaVCF.R tests/testthat/test_ConvertICAMSCatalogToSigPro.R tests/testthat/test_processing_empty_vcfs.R tests/testthat/test_PyrPenta.R tests/testthat/test_TransRownames.ID.PCAWG.SigPro.R tests/testthat/test_CheckAndFixChrNamesForTransRanges.R tests/testthat/test_RevcSBS96.R tests/testthat/test_ID_fns.R tests/testthat/test_PlotCatalog.SBS96Catalog.R tests/testthat/test_CheckAndFixChrNames.R tests/testthat/test_VCFsToCatalogAndPlotToPdf.R tests/testthat/test_ReadWriteCatalog.R tests/testthat/test_ReadVCFError.R tests/testthat/test_cbind_catalogs.R tests/testthat/test_MakeCatalogFromMutectGRCh38VCF.R tests/testthat/test_ReadCatalogError.R tests/testthat/test_methods_for_subsetting_catalogs.R tests/testthat/test_1VCFFilesToZipFile.R tests/testthat/test_AddSeqContext.R tests/testthat/test_PlotCatalog.IndelCatalog.R tests/testthat/test_PlotCatalogToPdf.SBS96Catalog.R tests/testthat/test_PlotCatalogToPdf.DBS136Catalog.R tests/testthat/test_Read_and_Split_VCFs.R tests/testthat/test_ReadVCF.R
tests/testthat/testdata/BTSG_WGS_PCAWG.dbs.78.csv
tests/testthat/testdata/BTSG_WGS_PCAWG.indels.csv
tests/testthat/testdata/regress.cat.dbs.144.csv
tests/testthat/testdata/Strelka.ID.GRCh38.vcf
tests/testthat/testdata/Strelka.SBS.GRCm38.vcf
tests/testthat/testdata/Strelka.SBS.GRCh38.vcf
tests/testthat/testdata/BTSG_WGS_PCAWG.sbs.96.csv
tests/testthat/testdata/regress.cat.sbs.96.tsv
tests/testthat/testdata/Strelka.mixed.GRCh37.vcf
tests/testthat/testdata/Strelka-mult-alt.vcf
tests/testthat/testdata/regress.cat.sbs.96.bad.row.names.csv
tests/testthat/testdata/Strelka.colname.VAF.vcf
tests/testthat/testdata/regress.cat.dbs.136.csv
tests/testthat/testdata/BTSG_WGS_PCAWG.sbs.192.csv
tests/testthat/testdata/Mutect.GRCh38.vcf
tests/testthat/testdata/sigProfiler_ID_signatures.csv
tests/testthat/testdata/CopyOfBTSG_WGS_PCAWG.dbs.78.csv
tests/testthat/testdata/SBS.GRCh37.variantcaller.unknown.vcf
tests/testthat/testdata/HepG2.dbs.136.csv
tests/testthat/testdata/Strelka.colname.strand.vcf
tests/testthat/testdata/BTSG_WGS_PCAWG.sbs.1536.csv
tests/testthat/testdata/Mutect.GRCm38.vcf
tests/testthat/testdata/create_one_col_delete_test.Rdata
tests/testthat/testdata/regress.cat.sbs.1536.csv
tests/testthat/testdata/test_AddSeqContext.Rdata
tests/testthat/testdata/create_one_col_insert_test.Rdata
tests/testthat/testdata/regress.cat.sbs.96.csv
tests/testthat/testdata/test_AnnotateIDVCF.Rdata
tests/testthat/testdata/regress.cat.sbs.96.one.column.csv
tests/testthat/testdata/HepG2.dbs.144.csv
tests/testthat/testdata/regress.cat.sbs.192.csv
tests/testthat/testdata/Strelka.ID.GRCm38.vcf
tests/testthat/testdata/PCAWGSig_0.0.3.9005.RDa
tests/testthat/testdata/regress.cat.dbs.78.csv
tests/testthat/testdata/SigPro-Cat/21BRCA.SBS96.tsv
tests/testthat/testdata/SigPro-Cat/21BRCA.DBS78.tsv
tests/testthat/testdata/SigPro-Cat/Strelka.ID.GRCh37.s1.ID96.tsv
tests/testthat/testdata/SigPro-Cat/Strelka.ID.GRCh37.s1.ID83.tsv
tests/testthat/testdata/Mutect-GRCh37/Mutect.GRCh37.s4.vcf
tests/testthat/testdata/Mutect-GRCh37/Mutect.GRCh37.s2.vcf
tests/testthat/testdata/Mutect-GRCh37/Mutect.GRCh37.s5.vcf
tests/testthat/testdata/Mutect-GRCh37/Mutect.GRCh37.s3.vcf
tests/testthat/testdata/Mutect-GRCh37/Mutect.GRCh37.s1.vcf
tests/testthat/testdata/COSMIC-Cat/COSMIC_SBS1_SBS96.csv
tests/testthat/testdata/COSMIC-Cat/COSMIC_SBS85_SBS96.csv
tests/testthat/testdata/COSMIC-Cat/COSMIC_ID1_ID96.csv
tests/testthat/testdata/COSMIC-Cat/COSMIC_DBS1_DBS78.csv
tests/testthat/testdata/COSMIC-Cat/COSMIC_SBS1_TSB192.csv
tests/testthat/testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s5.vcf
tests/testthat/testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s2.vcf
tests/testthat/testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s1.vcf
tests/testthat/testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s3.vcf
tests/testthat/testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s4.vcf
tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.s4.vcf
tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.s3.vcf
tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.s1.vcf
tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.s2.vcf
tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.s5.vcf
data/trans.ranges.GRCh38.rda
data/all.abundance.rda
data/trans.ranges.GRCh37.rda
data/gene.expression.data.HepG2.rda
data/gene.expression.data.MCF10A.rda
data/catalog.row.order.rda
data/trans.ranges.GRCm38.rda
man/TestMakeCatalogFromMutectVCFs.Rd man/RenameColumnsWithNameStrand.Rd man/FindMaxRepeatDel.Rd man/SplitListOfMutectVCFs.Rd man/VCFsToIDCatalogs.Rd man/CreateOneColSBSMatrix.Rd man/AnnotateIDVCF.Rd man/AddAndCheckSBSClassInVCF.Rd man/TestMakeCatalogFromStrelkaIDVCFs.Rd man/CreateTetranucAbundance.Rd man/StandardChromNameNew.Rd man/VCFsToZipFile.Rd man/IsGRCm38.Rd man/as.catalog.Rd man/InferAbundance.Rd man/CheckDBSClassInVCF.Rd man/ReadDukeNUSCat192.Rd man/ReadCatalog.Rd man/InferRownames.Rd man/TestMakeCatalogFromStrelkaSBSVCFs.Rd man/SplitOneVCF.Rd man/CheckAndReturnSBSMatrix.Rd man/Unstaple78.Rd man/GetMutationLoadsFromStrelkaSBSVCFs.Rd man/PlotPPMToPdf.Rd man/ICAMS.Rd man/CreateOnePPMFromSBSVCF.Rd man/Canonicalize1ID.Rd man/ReadStapleGT96SBS.Rd man/StopIfRegionIllegal.Rd man/CreateStrandedDinucAbundance.Rd man/MutectVCFFilesToCatalogAndPlotToPdf.Rd man/CreateOneColDBSMatrix.Rd man/MutectVCFFilesToZipFile.Rd man/AnnotateSBSVCF.Rd man/revc.Rd man/all.abundance.Rd man/CreateTransRanges.Rd man/VCFsToCatalogs.Rd man/StrelkaIDVCFFilesToCatalogAndPlotToPdf.Rd man/PlotPPM.Rd man/RenameColumnsWithNameVAF.Rd man/IsGRCh37.Rd man/TestPlotCatCOMPOSITE.Rd man/VCFsToSBSCatalogs.Rd man/AddTranscript.Rd man/MutectVCFFilesToCatalog.Rd man/ReadStrelkaIDVCF.Rd man/CheckAndReturnIDMatrix.Rd man/VCFsToZipFileXtra.Rd man/TransRownames.ID.SigPro.PCAWG.Rd man/ReadMutectVCFs.Rd man/CreateOneColIDMatrix.Rd man/GetVAF.Rd man/CheckAndReturnIDCatalog.Rd man/StrelkaIDVCFFilesToCatalog.Rd man/ReadAndSplitMutectVCFs.Rd man/CheckAndReturnSBSCatalogs.Rd man/VCFsToDBSCatalogs.Rd man/CanonicalizeID.Rd man/IsGRCh38.Rd man/StopIfCatalogTypeIllegal.Rd man/GenerateKmer.Rd man/WriteCatalog.Rd man/CollapseCatalog.Rd man/ReadAndSplitStrelkaSBSVCFs.Rd man/CheckSBSClassInVCF.Rd man/PlotTransBiasGeneExp.Rd man/AddAndCheckDBSClassInVCF.Rd man/AddDBSClass.Rd man/PlotTransBiasGeneExpToPdf.Rd man/CalBaseCountsFrom3MerAbundance.Rd man/GetCustomKmerCounts.Rd man/RevcSBS96.Rd man/AddSeqContext.Rd man/StopIfTranscribedRegionIllegal.Rd man/GeneExpressionData.Rd man/StopIfNrowIllegal.Rd man/Restaple1536.Rd man/CalculateNumberOfSpace.Rd man/TransRownames.ID.PCAWG.SigPro.Rd man/InferCatalogClassPrefix.Rd man/ReadCatalogInternal.Rd man/ReadCatalogErrReturn.Rd man/VCFsToCatalogsAndPlotToPdf.Rd man/CheckAndReturnDBSMatrix.Rd man/CreatePentanucAbundance.Rd man/ReadStrelkaSBSVCFs.Rd man/SplitSBSVCF.Rd man/SplitListOfStrelkaSBSVCFs.Rd man/WriteCat.Rd man/Unstaple1536.Rd man/StandardChromName.Rd man/FindDelMH.Rd man/MakeDataFrameFromVCF.Rd man/CheckAndFixChrNamesForTransRanges.Rd man/TCFromCouSigCou.Rd man/GenerateEmptyKmerCounts.Rd man/MakeVCFDBSdf.Rd man/Canonicalize1INS.Rd man/AddSBSClass.Rd man/CreateDinucAbundance.Rd man/StrelkaSBSVCFFilesToZipFile.Rd man/ConvertICAMSCatalogToSigProSBS96.Rd man/GetMutationLoadsFromMutectVCFs.Rd man/CreateExomeStrandedRanges.Rd man/SplitStrelkaSBSVCF.Rd man/SplitListOfVCFs.Rd man/PlotCatalog.Rd man/CheckAndReorderRownames.Rd man/StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd man/ReadBedRanges.Rd man/StrelkaSBSVCFFilesToCatalog.Rd man/CreateTrinucAbundance.Rd man/GetStrandedKmerCounts.Rd man/CreatePPMFromSBSVCFs.Rd man/GetConsensusVAF.Rd man/ReadVCF.Rd man/CatalogRowOrder.Rd man/CheckSeqContextInVCF.Rd man/ReadTranscriptRanges.Rd man/ReadVCFs.Rd man/Unstaple96.Rd man/Plot96PartOfCompositeToPDF.Rd man/SplitOneMutectVCF.Rd man/InferCatalogInfo.Rd man/GetMutationLoadsFromStrelkaIDVCFs.Rd man/GetGenomeKmerCounts.Rd man/NormalizeGenomeArg.Rd man/FindMaxRepeatIns.Rd man/ReadStrelkaIDVCFs.Rd man/AnnotateDBSVCF.Rd man/CheckAndFixChrNames.Rd man/ReadMutectVCF.Rd man/RemoveRangesOnBothStrand.Rd man/StrelkaIDVCFFilesToZipFile.Rd man/TransformCatalog.Rd man/ReadAndSplitVCFs.Rd man/TranscriptRanges.Rd man/RevcDBS144.Rd man/AddRunInformation.Rd man/CheckAndReturnDBSCatalogs.Rd man/Restaple96.Rd man/Canonicalize1Del.Rd man/WriteCatalogIndelSigPro.Rd man/GetSequenceKmerCounts.Rd man/PlotCatalogToPdf.Rd man/ReadStrelkaSBSVCF.Rd man/CreateStrandedTrinucAbundance.Rd man/TCFromDenSigDen.Rd
man/figures/README-pressure-1.png
ICAMS documentation built on June 22, 2024, 6:47 p.m.

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