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SnpArrays

Compressed storage for SNP data

https://github.com/openmendel/snparrays.jl

Science Score: 77.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov, zenodo.org
  • ✓
    Committers with academic emails
    6 of 12 committers (50.0%) from academic institutions
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (13.8%) to scientific vocabulary

Keywords

julia openmendel plink snps

Keywords from Contributors

julialang interpretability standardization online-algorithms onlinestats stochastic-approximation streaming-data hack
Last synced: 6 months ago · JSON representation ·

Repository

Compressed storage for SNP data

Basic Info
Statistics
  • Stars: 45
  • Watchers: 4
  • Forks: 9
  • Open Issues: 29
  • Releases: 25
Topics
julia openmendel plink snps
Created almost 10 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

SnpArrays.jl

| Documentation | Build Status | Code Coverage | Citation | |-------------------|------------------|--------------------|--------------------| | | build Actions Status | Coverage Status codecov | DOI |

Routines for reading and manipulating compressed storage of biallelic SNP (Single-Nucleotide Polymorphism) data.

Data from genome-wide association studies (GWAS) are often saved as a PLINK binary biallelic genotype table or .bed file. To be useful, such files should be accompanied by a .fam file, containing metadata on the rows of the table, and a .bim file, containing metadata on the columns. The .fam and .bim files are in tab-separated format.

Linear algebra operations on the PLINK formatted data now support multi-threading and GPU (CUDA) computing.

Installation

This package requires Julia v1.5 or later, which can be obtained from https://julialang.org/downloads/ or by building Julia from the sources in the https://github.com/JuliaLang/julia repository.

This package is registered in the default Julia package registry, and can be installed through standard package installation procedure. julia using Pkg pkg"add SnpArrays" Use the backspace key to return to the Julia REPL.

Citation

If you use OpenMendel analysis packages in your research, please cite the following reference in the resulting publications:

Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. OPENMENDEL: a cooperative programming project for statistical genetics. Hum Genet. 2020 Jan;139(1):61-71. doi: 10.1007/s00439-019-02001-z. Epub 2019 Mar 26. PMID: 30915546; PMCID: PMC6763373.

Acknowledgments

Current implementation incorporates ideas in the package BEDFiles.jl by Doug Bates (@dmbates).

Chris Elrod (@chriselrod) helped us accelerate CPU linear algebra through his great support of LoopVectorization.jl package.

This project has been supported by the National Institutes of Health under awards R01GM053275, R01HG006139, R25GM103774, and 1R25HG011845.

Owner

  • Name: OpenMendel
  • Login: OpenMendel
  • Kind: organization

Modern Statistical Genetics Software

Citation (CITATION.bib) 

@article{zhou2020openmendel,
  title={{OpenMendel}: a cooperative programming project for statistical genetics},
  author={Zhou, Hua and Sinsheimer, Janet S and Bates, Douglas M and Chu, Benjamin B and German, Christopher A and Ji, Sarah S and Keys, Kevin L and Kim, Juhyun and Ko, Seyoon and Mosher, Gordon D and others},
  journal={Human genetics},
  volume={139},
  number={1},
  pages={61--71},
  year={2020},
  publisher={Springer}
}

GitHub Events

Total
  • Create event: 3
  • Commit comment event: 3
  • Release event: 1
  • Watch event: 1
  • Issue comment event: 9
  • Push event: 299
  • Pull request event: 4
Last Year
  • Create event: 3
  • Commit comment event: 3
  • Release event: 1
  • Watch event: 1
  • Issue comment event: 9
  • Push event: 299
  • Pull request event: 4

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 339
  • Total Committers: 12
  • Avg Commits per committer: 28.25
  • Development Distribution Score (DDS): 0.442
Past Year
  • Commits: 3
  • Committers: 2
  • Avg Commits per committer: 1.5
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
Hua Zhou h****u@u****u 189
Seyoon Ko s****7@s****r 96
jcpapp j****p@m****u 13
github-actions[bot] 4****] 8
Chris German g****3@u****u 8
Benjamin Chu b****9@h****m 7
Josh Day e****y@g****m 6
Jeanette Papp j****p@u****u 5
Alfonso Landeros a****s@u****u 3
Marc Suchard m****d@u****u 2
BrendonChau 4****u 1
Andreas Noack a****n@g****m 1
Committer Domains (Top 20 + Academic)
ucla.edu: 5 mednet.ucla.edu: 1 snu.ac.kr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 50
  • Total pull requests: 68
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 23 days
  • Total issue authors: 12
  • Total pull request authors: 7
  • Average comments per issue: 2.74
  • Average comments per pull request: 1.54
  • Merged pull requests: 44
  • Bot issues: 0
  • Bot pull requests: 24
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kose-y (21)
  • biona001 (12)
  • Hua-Zhou (6)
  • mmkim1210 (2)
  • olivierlabayle (2)
  • espenmei (1)
  • BrendonChau (1)
  • Uljibuh (1)
  • alanderos91 (1)
  • richgill8 (1)
  • github-actions[bot] (1)
  • pdimens (1)
  • JuliaTagBot (1)
Pull Request Authors
  • kose-y (30)
  • github-actions[bot] (22)
  • biona001 (9)
  • Hua-Zhou (2)
  • BrendonChau (2)
  • dohyunkim116 (1)
  • alanderos91 (1)
Top Labels
Issue Labels
help wanted (4) feature request (3) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • julia 96 total
  • Total dependent packages: 9
  • Total dependent repositories: 1
  • Total versions: 13
juliahub.com: SnpArrays

Compressed storage for SNP data

  • Versions: 13
  • Dependent Packages: 9
  • Dependent Repositories: 1
  • Downloads: 96 Total
Rankings
Dependent repos count: 7.8%
Dependent packages count: 7.8%
Average: 11.0%
Forks count: 13.4%
Stargazers count: 15.0%
Last synced: 6 months ago

Dependencies

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