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musicatk

Mutational Signature Comprehensive Analysis Toolkit


Bioconductor version: Release (3.19)

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.

Author: Aaron Chevalier [aut] (0000-0002-3968-9250), Joshua D. Campbell [aut, cre]

Maintainer: Joshua D. Campbell <camp at bu.edu>

Citation (from within R, enter citation("musicatk")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("musicatk")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("musicatk")
Mutational Signature Comprehensive Analysis Toolkit HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiologicalQuestion, Software, SomaticMutation, VariantAnnotation
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License LGPL-3
Depends R (>= 4.0.0), 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, deconstructSigs, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1)
System Requirements
URL
Bug Reports https://github.com/campbio/musicatk/issues
See More
Suggests TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr
Linking To
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Depends On Me
Imports Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package musicatk_1.14.0.tar.gz
Windows Binary musicatk_1.14.0.zip
macOS Binary (x86_64) musicatk_1.14.0.tgz
macOS Binary (arm64) musicatk_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/musicatk
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/musicatk
Bioc Package Browser https://code.bioconductor.org/browse/musicatk/
Package Short Url https://bioconductor.org/packages/musicatk/
Package Downloads Report Download Stats