Package: musicatk
Type: Package
Title: Mutational Signature Comprehensive Analysis Toolkit
Version: 2.4.0
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
        libwebp-dev libxml2-dev libssl-dev perl libx11-dev xz-utils
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:03:52 UTC
RemoteUrl: https://github.com/bioc/musicatk
RemoteRef: RELEASE_3_22
RemoteSha: a2d2204ab1a912966554a84fb4438e47dfc45db4
NeedsCompilation: no
Packaged: 2026-03-12 09:24:19 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:
    <https://orcid.org/0000-0003-0780-8662>)
Maintainer: Joshua D. Campbell <camp@bu.edu>
Built: R 4.5.2; ; 2026-03-12 09:30:01 UTC; windows
