Other packages > Find by keyword >

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", "3.0.11")



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: 2025-06-15
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 3.0.11, https://cran.r-project.org/web/packages/ICAMS. Accessed 16 Oct. 2026.
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), 2.3.12 (2024-02-09 16:20), 3.0.11 (2025-06-15 02:30), (2026-07-09 08:06)
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
ICAMS  
In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')
Analysis and visualization of experimentally elucidated mutational signatures -- the kind of analys ...
Download / Learn more Package Citations See dependency  
micompr  
Multivariate Independent Comparison of Observations
A procedure for comparing multivariate samples associated with different groups. It uses principal ...
Download / Learn more Package Citations See dependency  
stpm  
Stochastic Process Model for Analysis of Longitudinal and Time-to-Event Outcomes
Utilities to estimate parameters of the models with survival functions induced by stochastic covar ...
Download / Learn more Package Citations See dependency  
TreeDimensionTest  
Trajectory Presence and Heterogeneity in Multivariate Data
Testing for trajectory presence and heterogeneity on multivariate data. Two statistical methods (Te ...
Download / Learn more Package Citations See dependency  
MindOnStats  
Data sets included in Utts and Heckard's Mind on Statistics
66 data sets that were imported using read.table() where appropriate but more commonly after convert ...
Download / Learn more Package Citations See dependency  

29,000

R Packages

247,686

Dependencies

76,729

Author Associations

29,001

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA