RESOLVE

DOI: 10.18129/B9.bioc.RESOLVE  

RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes

Bioconductor version: Release (3.16)

Cancer is a genetic disease caused by somatic mutations in genes controlling key biological functions such as cellular growth and division. Such mutations may arise both through cell-intrinsic and exogenous processes, generating characteristic mutational patterns over the genome named mutational signatures. The study of mutational signatures have become a standard component of modern genomics studies, since it can reveal which (environmental and endogenous) mutagenic processes are active in a tumor, and may highlight markers for therapeutic response. Mutational signatures computational analysis presents many pitfalls. First, the task of determining the number of signatures is very complex and depends on heuristics. Second, several signatures have no clear etiology, casting doubt on them being computational artifacts rather than due to mutagenic processes. Last, approaches for signatures assignment are greatly influenced by the set of signatures used for the analysis. To overcome these limitations, we developed RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization), a framework that allows the efficient extraction and assignment of mutational signatures. RESOLVE implements a novel algorithm that enables (i) the efficient extraction, (ii) exposure estimation, and (iii) confidence assessment during the computational inference of mutational signatures.

Author: Daniele Ramazzotti [aut] , Luca De Sano [cre, aut]

Maintainer: Luca De Sano <luca.desano at gmail.com>

Installation

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

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

BiocManager::install("RESOLVE")

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("RESOLVE")

 

HTML	R Script	RESOLVE.html
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiomedicalInformatics, Software, SomaticMutation
Version	1.0.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	file LICENSE
Depends	R (>= 3.5.0), NMF
Imports	Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, cluster, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, nnls, parallel, reshape2
LinkingTo
Suggests	BiocGenerics, BiocStyle, testthat, knitr
SystemRequirements
Enhances
URL	https://github.com/danro9685/RESOLVE
BugReports	https://github.com/danro9685/RESOLVE/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	RESOLVE_1.0.0.tar.gz
Windows Binary	RESOLVE_1.0.0.zip
macOS Binary (x86_64)	RESOLVE_1.0.0.tgz
macOS Binary (arm64)	RESOLVE_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RESOLVE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RESOLVE
Bioc Package Browser	https://code.bioconductor.org/browse/RESOLVE/
Package Short Url	https://bioconductor.org/packages/RESOLVE/
Package Downloads Report	Download Stats