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SNPassoc

Genetic association studies

https://github.com/isglobal-brge/snpassoc

Science Score: 13.0%

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
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (3.1%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Genetic association studies

Basic Info
  • Host: GitHub
  • Owner: isglobal-brge
  • Language: R
  • Default Branch: master
  • Size: 1.87 MB
Statistics
  • Stars: 16
  • Watchers: 2
  • Forks: 6
  • Open Issues: 5
  • Releases: 0
Created about 9 years ago · Last pushed almost 2 years ago
Metadata Files
Readme

README.md

SNPassoc

This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated.

Owner

  • Name: Bioinformatic Research Group in Epidemiology (BRGE)
  • Login: isglobal-brge
  • Kind: user
  • Location: Barcelona, Spain
  • Company: Barcelona Institute for Global Health (ISGlobal)

Bioinformatics, biostatistics, omic data integration, advanced statistical methods, R programming

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Push event: 6
Last Year
  • Issues event: 2
  • Watch event: 1
  • Push event: 6

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 57
  • Total Committers: 3
  • Avg Commits per committer: 19.0
  • Development Distribution Score (DDS): 0.281
Past Year
  • Commits: 8
  • Committers: 2
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.375
Top Committers
Name Email Commits
Bioinformatic Research Group in Epidemiology (BRGE) j****z@i****g 41
dpelegri d****i@g****m 15
Xavier Escribà Montagut x****t@g****m 1
Committer Domains (Top 20 + Academic)
isglobal.org: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 7
  • Total pull requests: 9
  • Average time to close issues: 25 days
  • Average time to close pull requests: about 16 hours
  • Total issue authors: 7
  • Total pull request authors: 3
  • Average comments per issue: 0.86
  • Average comments per pull request: 0.0
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Eduardo-Auer (1)
  • Lidija0710 (1)
  • ramiromagno (1)
  • nampharmd (1)
  • antoniaprn (1)
  • VoronDM (1)
  • MboiTui (1)
Pull Request Authors
  • dpelegri (6)
  • VoronDM (4)
  • ESCRI11 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 1,489 last-month
  • Total dependent packages: 3
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 37
  • Total maintainers: 1
cran.r-project.org: SNPassoc

SNPs-Based Whole Genome Association Studies

  • Versions: 34
  • Dependent Packages: 2
  • Dependent Repositories: 1
  • Downloads: 1,489 Last month
Rankings
Forks count: 12.3%
Dependent packages count: 13.8%
Stargazers count: 14.7%
Downloads: 15.7%
Average: 16.1%
Dependent repos count: 24.2%
Maintainers (1)
dolors.pelegri@isglobal.org
Last synced: 12 months ago
conda-forge.org: r-snpassoc
  • Versions: 3
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Average: 31.4%
Dependent repos count: 34.0%
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • BiocStyle * imports
  • Biostrings * imports
  • GenomicRanges * imports
  • IRanges * imports
  • S4Vectors * imports
  • TxDb.Hsapiens.UCSC.hg19.knownGene * imports
  • VariantAnnotation * imports
  • ggplot2 * imports
  • haplo.stats * imports
  • mvtnorm * imports
  • org.Hs.eg.db * imports
  • parallel * imports
  • plyr * imports
  • poisbinom * imports
  • survival * imports
  • tidyr * imports
  • BSgenome * suggests
  • BSgenome.Hsapiens.NCBI.GRCh38 * suggests
  • GenomicScores * suggests
  • MafDb.1Kgenomes.phase3.GRCh38 * suggests
  • SNPlocs.Hsapiens.dbSNP144.GRCh38 * suggests
  • biomaRt * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests