RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from https://www.bioconductor.org/packages/release/bioc/html/musicatk.html below:

Bioconductor - musicatk

musicatk

This is the released version of musicatk; for the devel version, see musicatk.

Mutational Signature Comprehensive Analysis Toolkit

Bioconductor version: Release (3.21)

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] (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: 0000-0003-0780-8662

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

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

To install this package, start R (version "4.5") 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 2.2.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License LGPL-3 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, conclust 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 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.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4