musicatk

DOI: 10.18129/B9.bioc.musicatk    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see musicatk.

Mutational Signature Comprehensive Analysis Toolkit

Bioconductor version: 3.15

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

Maintainer: Aaron Chevalier <atgc at bu.edu>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Mutational Signature Comprehensive Analysis Toolkit
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiologicalQuestion, Software, SomaticMutation, VariantAnnotation
Version	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	LGPL-3
Depends	R (>= 4.0.0), NMF
Imports	SummarizedExperiment, VariantAnnotation, cowplot, 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, withr, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, shinydashboard, sortable, maftools, shiny, shinyjs, shinyalert, shinybusy, shinyBS, TCGAbiolinks, shinyjqui, stringi
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr
SystemRequirements
Enhances
URL
BugReports	https://github.com/campbio/musicatk/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	musicatk_1.6.0.tar.gz
Windows Binary	musicatk_1.6.0.zip
macOS Binary (x86_64)	musicatk_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/musicatk
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/musicatk
Package Short Url	https://bioconductor.org/packages/musicatk/
Package Downloads Report	Download Stats