musicatk
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see musicatk.
Mutational Signature Comprehensive Analysis Toolkit
Bioconductor version: 3.14
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>
citation("musicatk")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, Software, SomaticMutation, VariantAnnotation |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | LGPL-3 |
| Depends | R (>= 4.0.0), NMF |
| Imports | SummarizedExperiment, VariantAnnotation, 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/campbio/musicatk/issues |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | musicatk_1.4.0.tar.gz |
| Windows Binary | musicatk_1.4.0.zip |
| macOS 10.13 (High Sierra) | musicatk_1.4.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |