Package: RESOLVE
Version: 1.15.0
Date: 2026-03-09
Title: RESOLVE: An R package for the efficient analysis of mutational
        signatures from cancer genomes
Authors@R: c(
    person("Daniele", "Ramazzotti", role=c("aut"),email="daniele.ramazzotti@unimib.it",
                comment = c(ORCID = "0000-0002-6087-2666")),
    person("Luca", "De Sano", role=c("cre","aut"), email="luca.desano@gmail.com",
                comment = c(ORCID = "0000-0002-9618-3774")))
Depends: R (>= 4.1.0)
Imports: Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5,
        cluster, data.table, GenomeInfoDb, GenomicRanges, glmnet,
        ggplot2, gridExtra, IRanges, lsa, MutationalPatterns, nnls,
        parallel, reshape2, S4Vectors, RhpcBLASctl, survival
Suggests: BiocGenerics, BiocStyle, testthat, knitr
Description: 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.
Encoding: UTF-8
License: file LICENSE
URL: https://github.com/danro9685/RESOLVE
BugReports: https://github.com/danro9685/RESOLVE/issues
biocViews: BiomedicalInformatics, SomaticMutation
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:59:14 UTC
RemoteUrl: https://github.com/bioc/RESOLVE
RemoteRef: HEAD
RemoteSha: 71166a909848d9e3d67ed945b072243fc66ebaea
NeedsCompilation: no
Packaged: 2026-07-10 05:59:23 UTC; root
Author: Daniele Ramazzotti [aut] (ORCID:
    <https://orcid.org/0000-0002-6087-2666>),
  Luca De Sano [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-9618-3774>)
Maintainer: Luca De Sano <luca.desano@gmail.com>