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RESOLVE

RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization) is an R package for the efficient extraction and assignment of mutational signatures from cancer genomes.

https://github.com/danro9685/resolve

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.4%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization) is an R package for the efficient extraction and assignment of mutational signatures from cancer genomes.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 5
Created almost 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

RESOLVE

| Branch | Status | | --- | --- | | master | R-CMD-check-bioc | | development | R-CMD-check-bioc |

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. Additionally, RESOLVE enables the precise stratification of cancer genomes based on mutational signatures, allowing for the identification of key signatures that drive specific cancer subtypes. Beyond de novo extraction, assignment, and confidence estimation, RESOLVE also supports patient clustering, survival analysis to identify risk groups linked to distinct mutational processes, and the investigation of associations between mutational signatures and driver gene mutations. These advanced capabilities offer deeper insights into tumorigenesis mechanisms, their prognostic relevance, and potential therapeutic targets.

Owner

  • Name: Daniele Ramazzotti
  • Login: danro9685
  • Kind: user
  • Location: Milano, Italy
  • Company: University of Milano-Bicocca, Milano, Italy

Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy

GitHub Events

Total
  • Release event: 2
  • Push event: 15
  • Create event: 2
Last Year
  • Release event: 2
  • Push event: 15
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 175
  • Total Committers: 3
  • Avg Commits per committer: 58.333
  • Development Distribution Score (DDS): 0.069
Past Year
  • Commits: 125
  • Committers: 3
  • Avg Commits per committer: 41.667
  • Development Distribution Score (DDS): 0.08
Top Committers
Name Email Commits
danro9685 d****i@y****m 163
luca-dex l****o@g****m 10
J Wokaty j****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 1
  • Total pull requests: 3
  • Average time to close issues: about 1 hour
  • Average time to close pull requests: about 6 hours
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: about 1 hour
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • riccardobergamin (1)
Pull Request Authors
  • luca-dex (3)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 5,499 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: RESOLVE

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

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 5,499 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 32.0%
Downloads: 96.0%
Maintainers (1)
luca.desano@gmail.com
Last synced: 11 months ago

Dependencies

.github/workflows/check-development.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v2 composite
.github/workflows/check-master.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v2 composite
DESCRIPTION cran
  • R >= 4.1.0 depends
  • BSgenome * imports
  • BSgenome.Hsapiens.1000genomes.hs37d5 * imports
  • Biostrings * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • IRanges * imports
  • data.table * imports
  • ggplot2 * imports
  • glmnet * imports
  • gridExtra * imports
  • lsa * imports
  • methods * imports
  • nnls * imports
  • parallel * imports
  • reshape2 * imports
  • BiocGenerics * suggests
  • BiocStyle * suggests
  • knitr * suggests
  • testthat * suggests