Package: musicatk Type: Package Title: Mutational Signature Comprehensive Analysis Toolkit Version: 2.7.0 Authors@R: c(person("Aaron", "Chevalier", email = "atgc@bu.edu", role = "aut", comment = c(ORCHID = "0000-0002-3968-9250")), person("Natasha", "Gurevich", email = "nqg@bu.edu", role = "aut", comment = c(ORCHID = "0000-0002-0747-6840")), person("Tao", "Guo", email = "guo1241@gmail.com", role = "aut", comment = c(ORCHID = "0009-0005-8960-9203")), person(given=c("Joshua","D."), family="Campbell", email="camp@bu.edu", role=c("aut", "cre"), comment = c(ORCID = "0000-0003-0780-8662"))) Description: Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3. License: LGPL-3 URL: https://www.camplab.net/musicatk/ BugReports: https://github.com/campbio/musicatk/issues Encoding: UTF-8 LazyData: TRUE biocViews: Software, BiologicalQuestion, SomaticMutation, VariantAnnotation Depends: R (>= 4.4.0), NMF Imports: SummarizedExperiment, VariantAnnotation, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1), scales Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr RoxygenNote: 7.3.2 VignetteBuilder: knitr Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev libfribidi-dev make libgsl0-dev libharfbuzz-dev libbz2-dev libicu-dev libjpeg-dev liblzma-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev libssl-dev perl libx11-dev xz-utils zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:54:13 UTC RemoteUrl: https://github.com/bioc/musicatk RemoteRef: HEAD RemoteSha: 4eabe7f8aecc2a4490cd6b60178b9db348a92d5c NeedsCompilation: no Packaged: 2026-07-03 19:10:03 UTC; root Author: Aaron Chevalier [aut] (ORCHID: 0000-0002-3968-9250), Natasha Gurevich [aut] (ORCHID: 0000-0002-0747-6840), Tao Guo [aut] (ORCHID: 0009-0005-8960-9203), Joshua D. Campbell [aut, cre] (ORCID: ) Maintainer: Joshua D. Campbell