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ICAMS  

In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')
View on CRAN: Click here


Download and install ICAMS package within the R console
Install from CRAN:
install.packages("ICAMS")

Install from Github:
library("remotes")
install_github("cran/ICAMS")

Install by package version:
library("remotes")
install_version("ICAMS", "2.3.12")



Attach the package and use:
library("ICAMS")
Maintained by
Steve Rozen
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-07-11
Latest Update: 2024-02-09
Description:
Analysis and visualization of experimentally elucidated mutational signatures -- the kind of analysis and visualization in Boot et al., "In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors", Genome Research 2018, and "Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types", Genome Research 2020 . 'ICAMS' stands for In-depth Characterization and Analysis of Mutational Signatures. 'ICAMS' has functions to read in variant call files (VCFs) and to collate the corresponding catalogs of mutational spectra and to analyze and plot catalogs of mutational spectra and signatures. Handles both "counts-based" and "density-based" (i.e. representation as mutations per megabase) mutational spectra or signatures.
How to cite:
Steve Rozen (2019). ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS'). R package version 2.3.12, https://cran.r-project.org/web/packages/ICAMS. Accessed 03 Dec. 2024.
Previous versions and publish date:
2.0.7 (2019-07-11 14:53), 2.0.8 (2019-07-24 15:30), 2.0.10 (2019-12-13 11:20), 2.1.2 (2020-04-21 14:20), 2.2.3 (2020-09-18 15:00), 2.2.4 (2020-09-22 10:40), 2.3.10 (2021-04-03 15:50)
Other packages that cited ICAMS R package
View ICAMS citation profile
Other R packages that ICAMS depends, imports, suggests or enhances
Complete documentation for ICAMS
Functions, R codes and Examples using the ICAMS R package
Some associated functions: AddAndCheckDBSClassInVCF . AddAndCheckSBSClassInVCF . AddDBSClass . AddRunInformation . AddSBSClass . AddSeqContext . AddTranscript . AnnotateDBSVCF . AnnotateIDVCF . AnnotateSBSVCF . 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 . CreatePPMFromSBSVCFs . CreatePentanucAbundance . 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 . Restaple1536 . Restaple96 . 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 . TransRownames.ID.PCAWG.SigPro . TransRownames.ID.SigPro.PCAWG . TranscriptRanges . TransformCatalog . Unstaple1536 . Unstaple78 . Unstaple96 . VCFsToCatalogs . VCFsToCatalogsAndPlotToPdf . VCFsToDBSCatalogs . VCFsToIDCatalogs . VCFsToSBSCatalogs . VCFsToZipFile . VCFsToZipFileXtra . WriteCat . WriteCatalog . WriteCatalogIndelSigPro . all.abundance . as.catalog . revc . 
Some associated R codes: COMPOSITE.R . ICAMS.R . ID_functions.R . VCF_to_catalog_functions.R . chromosome_name_functions.R . data.R . infer_catalog_format.R . other_catalog_formats.R . plot.R . read_write_catalog.R . sequence_context_functions.R . shiny_related_functions.R . strandbias_functions.R . test_functions.R . utility_functions.R .  Full ICAMS package functions and examples
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