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Open Source Science

MoonlightR

https://github.com/elelab/moonlightr

Science Score: 36.0%

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
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 18 committers (5.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (3.7%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics bioconductor bioc tcga u24ca289073 core-package tcga-data integrative-analysis
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: ELELAB
  • Language: R
  • Default Branch: master
  • Size: 23.3 MB
Statistics
  • Stars: 17
  • Watchers: 4
  • Forks: 6
  • Open Issues: 0
  • Releases: 0
Created almost 10 years ago · Last pushed about 2 years ago
Metadata Files
Readme

README.md

Cancer Structural Biology Group, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark

Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Copenhagen

Repository associated to the publication:

Interpreting pathways to discover cancer driver genes with Moonlight. Colaprico A, Olsen C, Bailey MH, Odom GJ, Terkelsen T, Silva TC, Olsen AV, Cantini L, Zinovyev A, Barillot E, Noushmehr H, Bertoli G, Castiglioni I, Cava C, Bontempi G, Chen XS, Papaleo E. Nat Commun. 2020 Jan 3;11(1):69. doi: 10.1038/s41467-019-13803-0., PMID: 31900418

contacts for repository: Elena Papaleo, elpap-at-dtu.dk, elenap-at-cancer.dk; Matteo Tiberti: tiberti-at-cancer.dk

Identify oncogenes and tumor suppressor genes from genomic (gene expression) data.

Installation from Bioconductor

R if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("MoonlightR")

Installation from GitHub

R devtools::install_github(repo = "ibsquare/MoonlightR")

Owner

  • Name: ELELAB
  • Login: ELELAB
  • Kind: organization
  • Location: Copenhagen, Denmark

Cancer Structural Biology (DCRC) & Cancer System Biology (DTU), DK

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 141
  • Total Committers: 18
  • Avg Commits per committer: 7.833
  • Development Distribution Score (DDS): 0.589
Past Year
  • Commits: 12
  • Committers: 5
  • Avg Commits per committer: 2.4
  • Development Distribution Score (DDS): 0.75
Top Committers
Name Email Commits
torongs82 a****o@g****m 58
colsen c****n@u****e 22
Nitesh Turaga n****a@g****m 14
Matteo Tiberti m****i@g****m 12
Mona m****a@k****k 7
Tiago Chedraoui Silva t****m 5
Herve Pages h****s@f****g 5
lshep l****d@r****g 2
vobencha v****n@r****g 2
Hervé Pagès h****s@f****g 2
vobencha v****a@g****m 2
J Wokaty j****y@s****u 2
J Wokaty j****y 2
elenapapaleo e****8@g****m 2
Martin Morgan m****n@f****g 1
Astrid Saksager a****r@g****m 1
LiNk-NY m****9@g****m 1
Levi Waldron l****h@g****m 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 2 fhcrc.org: 2 sph.cuny.edu: 1 fredhutch.org: 1 kb-bioinfo01.cancer.dk: 1 ulb.ac.be: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 18
  • Total pull requests: 13
  • Average time to close issues: 9 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 7
  • Total pull request authors: 4
  • Average comments per issue: 1.11
  • Average comments per pull request: 0.0
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • mtiberti (7)
  • mona-n (3)
  • annarerra (2)
  • asaksager (2)
  • Pravithaks (2)
  • lwaldron (1)
  • Rahel14350 (1)
Pull Request Authors
  • mona-n (7)
  • mtiberti (5)
  • lwaldron (1)
  • asaksager (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 16,904 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: MoonlightR

Identify oncogenes and tumor suppressor genes from omics data

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 16,904 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 8.0%
Forks count: 8.8%
Average: 14.1%
Downloads: 53.7%
Maintainers (1)
tiberti@cancer.dk
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • doParallel * depends
  • foreach * depends
  • Biobase * imports
  • DOSE * imports
  • GEOquery * imports
  • HiveR * imports
  • RColorBrewer * imports
  • RISmed * imports
  • SummarizedExperiment * imports
  • TCGAbiolinks * imports
  • circlize * imports
  • clusterProfiler * imports
  • gplots * imports
  • grDevices * imports
  • graphics * imports
  • grid * imports
  • limma * imports
  • parmigene * imports
  • randomForest * imports
  • stats * imports
  • utils * imports
  • BiocStyle * suggests
  • devtools * suggests
  • knitr * suggests
  • png * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat * suggests