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RESOLVE

This is the development version of RESOLVE; for the stable release version, see RESOLVE.

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


Bioconductor version: Development (3.19)

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>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RESOLVE")

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

Documentation

Reference Manual PDF

Details

biocViews BiomedicalInformatics, Software, SomaticMutation
Version 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License file LICENSE
Depends R (>= 4.1.0)
Imports Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, methods, MutationalPatterns, nnls, parallel, reshape2, S4Vectors
System Requirements
URL https://github.com/danro9685/RESOLVE
Bug Reports https://github.com/danro9685/RESOLVE/issues
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Suggests BiocGenerics, BiocStyle, testthat, knitr
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Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/RESOLVE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RESOLVE
Package Short Url https://bioconductor.org/packages/RESOLVE/
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