{ "_id": "6a1acb0c1d7bb097a09ddc23", "Package": "LACHESIS", "Title": "Functions used to analyze early tumor evolution from whole\ngenome sequencing data", "Version": "1.1.0", "Authors@R": "c(\nperson(given = \"Verena\",\nfamily = \"Körber\",\nrole = c(\"aut\", \"cre\"),\nemail = \"verena.korber@ndcls.ox.ac.uk\",\ncomment = c(ORCID = \"0009-0005-3888-2648\")),\nperson(given = \"Anand\",\nfamily = \"Mayakonda\",\nrole = c(\"aut\"),\nemail = \"a.mayakonda@kitz-heidelberg.de\"),\nperson(given = \"Maximilia\",\nfamily = \"Eggle\",\nrole = c(\"aut\"),\nemail = \"maximilia.eggle@kitz-heidelberg.de\"))", "Description": "This package provides modalities to analyze tumor\nevolution from whole genome sequencing data. In particular, it\nprovides estimates of mutation densities at genomic segments\nand uses these to time the origin of the tumor.", "License": "GPL (>= 3)", "Copyright": "Verena Körber, Anand Mayakonda, Maximilia Eggle (2025)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "biocViews": "Software, StatisticalMethod, TimeCourse, Sequencing,\nWholeGenome, Survival, SomaticMutation", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "URL": "https://github.com/VerenaK90/LACHESIS", "BugReports": "https://github.com/VerenaK90/LACHESIS/issues", "Config/pak/sysreqs": "cmake make libicu-dev libjpeg-dev libpng-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:05:56 UTC", "RemoteUrl": "https://github.com/bioc/LACHESIS", "RemoteRef": "HEAD", "RemoteSha": "1b25ebaaaa1f26572d1cf19d2391e0316549eb7a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:55:37 UTC", "User": "root" }, "Author": "Verena Körber 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information", "Importing Variant Information (readVCF)", "Example: SNV calls obtained with Mutect", "Example: SNV calls obtained with Strelka", "Example: SNV calls obtained with the dkfz SNV calling workflow", "Plotting Variant Allele Frequencies (plotVAFdistr)", "Example", "Assigning copy number states to single nucleotide variants (nbImport)", "Assignment of mutational signatures", "Example using all variants from vcf file", "Example using variants associated with specific SBS mutational signatures from vcf file", "Plotting Imported Data (plotNB)", "Example using variants assosciated with specific SBS mutational signatures from vcf file", "Processing Clonal Mutations", "Counting Clonal Mutations (ClonalMutationalCounter)", "Normalizing Clonal Mutation Counts (normalizeCounts)", "Inferring Clonal Evolution", "Estimating Mutation Densities at ECA/MRCA (MRCA)", "Input Parameters", "Plotting Mutation Densities (plotMutationalDensities)", "Estimating Clonality per SNV 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