RESOLVE
RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes
Bioconductor version: Release (3.17)
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("RESOLVE")):
Installation
To install this package, start R (version "4.3") 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")| RESOLVE.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, Software, SomaticMutation |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (1 year) |
| 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 |
| Linking To | |
| Suggests | BiocGenerics, BiocStyle, testthat, knitr |
| System Requirements | |
| Enhances | |
| URL | https://github.com/danro9685/RESOLVE |
| Bug Reports | https://github.com/danro9685/RESOLVE/issues |
See More
| 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_1.2.0.tar.gz |
| Windows Binary | RESOLVE_1.2.0.zip |
| macOS Binary (x86_64) | RESOLVE_1.2.0.tgz |
| macOS Binary (arm64) | RESOLVE_1.2.0.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 |