Package: ICAMS 3.0.6

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

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, <doi:10.1101/gr.230219.117> and "Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types", Genome Research 2020 <doi:10.1101/gr.255620.119>. '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.

Authors:Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu, Mi Ni Huang, Jia Geng Chang

ICAMS_3.0.6.tar.gz
ICAMS_3.0.6.zip(r-4.5)ICAMS_3.0.6.zip(r-4.4)ICAMS_3.0.6.zip(r-4.3)
ICAMS_3.0.6.tgz(r-4.4-any)ICAMS_3.0.6.tgz(r-4.3-any)
ICAMS_3.0.6.tar.gz(r-4.5-noble)ICAMS_3.0.6.tar.gz(r-4.4-noble)
ICAMS_3.0.6.tgz(r-4.4-emscripten)ICAMS_3.0.6.tgz(r-4.3-emscripten)
ICAMS.pdf |ICAMS.html✨
ICAMS/json (API)
NEWS

# Install 'ICAMS' in R:
install.packages('ICAMS', repos = c('https://steverozen.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/steverozen/icams/issues

Datasets:

On CRAN:

45 exports 8 stars 1.65 score 77 dependencies 130 scripts 325 downloads

Last updated 2 years agofrom:a6dccbfe44. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-winERRORAug 27 2024
R-4.5-linuxERRORAug 27 2024
R-4.4-winERRORAug 27 2024
R-4.4-macERRORAug 27 2024
R-4.3-winERRORJul 28 2024
R-4.3-macERRORJul 28 2024

Exports:AnnotateDBSVCFAnnotateIDVCFAnnotateSBSVCFas.catalogCanonicalize1DelCollapse144CatalogTo78Collapse1536CatalogTo96Collapse192CatalogTo96FindDelMHFindMaxRepeatDelGetFreebayesVAFGetMutectVAFGetPCAWGConsensusVAFGetStrelkaVAFIsICAMSCatalogMutectVCFFilesToCatalogMutectVCFFilesToCatalogAndPlotToPdfMutectVCFFilesToZipFilePlotCatalogPlotCatalogToPdfPlotTransBiasGeneExpPlotTransBiasGeneExpToPdfReadAndSplitMutectVCFsReadAndSplitStrelkaSBSVCFsReadAndSplitVCFsReadCatalogReadStrelkaIDVCFsReadVCFsrevcSimpleReadVCFSplitListOfVCFsStrelkaIDVCFFilesToCatalogStrelkaIDVCFFilesToCatalogAndPlotToPdfStrelkaIDVCFFilesToZipFileStrelkaSBSVCFFilesToCatalogStrelkaSBSVCFFilesToCatalogAndPlotToPdfStrelkaSBSVCFFilesToZipFileTransformCatalogVCFsToCatalogsVCFsToCatalogsAndPlotToPdfVCFsToDBSCatalogsVCFsToIDCatalogsVCFsToSBSCatalogsVCFsToZipFileWriteCatalog

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeclicodetoolscpp11crayoncurldata.tableDelayedArraydplyrfansiformatRfutile.loggerfutile.optionsfuzzyjoingenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgeospheregluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpurrrR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowspSparseArraystringdiststringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLXVectoryamlzipzlibbioc

Readme and manuals

Help Manual

Help pageTopics
K-mer abundancesall.abundance
Add sequence context and transcript information to an in-memory DBS VCFAnnotateDBSVCF
Add sequence context to an in-memory ID (insertion/deletion) VCF, and confirm that they match the given reference genomeAnnotateIDVCF
Add sequence context and transcript information to an in-memory SBS VCFAnnotateSBSVCF
Create a catalog from a 'matrix', 'data.frame', or 'vector'as.catalog
Given a deletion and its sequence context, categorize itCanonicalize1Del
Standard order of row names in a catalogcatalog.row.order CatalogRowOrder
"Collapse" a catalogCollapse144CatalogTo78 Collapse1536CatalogTo96 Collapse192CatalogTo96 CollapseCatalog
Return the length of microhomology at a deletionFindDelMH
Return the number of repeat units in which a deletion is embeddedFindMaxRepeatDel
Example gene expression data from two cell linesgene.expression.data.HepG2 gene.expression.data.MCF10A GeneExpressionData
Extract the VAFs (variant allele frequencies) and read depth information from a VCF fileGetFreebayesVAF GetMutectVAF GetPCAWGConsensusVAF GetStrelkaVAF GetVAF
ICAMS: In-depth Characterization and Analysis of Mutational SignaturesICAMS
Check whether an R object contains one of the ICAMS catalog classesIsICAMSCatalog
*[Deprecated, use VCFsToCatalogs(variant.caller = "mutect") instead]* Create SBS, DBS and Indel catalogs from Mutect VCF filesMutectVCFFilesToCatalog
*[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller = "mutect") instead]* Create SBS, DBS and Indel catalogs from Mutect VCF files and plot them to PDFMutectVCFFilesToCatalogAndPlotToPdf
*[Deprecated, use VCFsToZipFile(variant.caller = "mutect") instead]* Create a zip file which contains catalogs and plot PDFs from Mutect VCF filesMutectVCFFilesToZipFile
Plot *one* spectrum or signaturePlotCatalog
Plot catalog to a PDF filePlotCatalogToPdf
Plot transcription strand bias with respect to gene expression valuesPlotTransBiasGeneExp
Plot transcription strand bias with respect to gene expression values to a PDF filePlotTransBiasGeneExpToPdf
*[Deprecated, use ReadAndSplitVCFs(variant.caller = "mutect") instead]* Read and split Mutect VCF filesReadAndSplitMutectVCFs
*[Deprecated, use ReadAndSplitVCFs(variant.caller = "strelka") instead]* Read and split Strelka SBS VCF filesReadAndSplitStrelkaSBSVCFs
Read and split VCF filesReadAndSplitVCFs
Read catalogReadCatalog
*[Deprecated, use ReadAndSplitVCFs(variant.caller = "strelka") instead]* Read Strelka ID (small insertions and deletions) VCF filesReadStrelkaIDVCFs
Read VCF filesReadVCFs
Reverse complement every string in 'string.vec'revc
Read a VCF file into a data frame with minimal processing.SimpleReadVCF
Split each VCF into SBS, DBS, and ID VCFs (plus VCF-like data frame with left-over rows)SplitListOfVCFs
*[Deprecated, use VCFsToCatalogs(variant.caller = "strelka") instead]* Create ID (small insertions and deletions) catalog from Strelka ID VCF filesStrelkaIDVCFFilesToCatalog
*[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller = "strelka") instead]* Create ID (small insertions and deletions) catalog from Strelka ID VCF files and plot them to PDFStrelkaIDVCFFilesToCatalogAndPlotToPdf
*[Deprecated, use VCFsToZipFile(variant.caller = "strelka") instead]* Create a zip file which contains ID (small insertions and deletions) catalog and plot PDF from Strelka ID VCF filesStrelkaIDVCFFilesToZipFile
*[Deprecated, use VCFsToCatalogs(variant.caller = "strelka") instead]* Create SBS and DBS catalogs from Strelka SBS VCF filesStrelkaSBSVCFFilesToCatalog
*[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller = "strelka") instead]* Create SBS and DBS catalogs from Strelka SBS VCF files and plot them to PDFStrelkaSBSVCFFilesToCatalogAndPlotToPdf
*[Deprecated, use VCFsToZipFile(variant.caller = "strelka") instead]* Create a zip file which contains catalogs and plot PDFs from Strelka SBS VCF filesStrelkaSBSVCFFilesToZipFile
Transcript ranges datatrans.ranges.GRCh37 trans.ranges.GRCh38 trans.ranges.GRCm38 TranscriptRanges
Transform between counts and density spectrum catalogs and counts and density signature catalogsTransformCatalog
Create SBS, DBS and Indel catalogs from VCFsVCFsToCatalogs
Create SBS, DBS and Indel catalogs from VCFs and plot them to PDFVCFsToCatalogsAndPlotToPdf
Create DBS catalogs from VCFsVCFsToDBSCatalogs
Create ID (small insertions and deletions) catalog from ID VCFsVCFsToIDCatalogs
Create SBS catalogs from SBS VCFsVCFsToSBSCatalogs
Create a zip file which contains catalogs and plot PDFs from VCFsVCFsToZipFile
Write a catalogWriteCatalog