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qtl2

QTL analysis software for high-dimensional data and complex cross designs

https://github.com/rqtl/qtl2

Science Score: 59.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

QTL analysis software for high-dimensional data and complex cross designs

Basic Info
  • Host: GitHub
  • Owner: rqtl
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage: https://kbroman.org/qtl2
  • Size: 44.9 MB
Statistics
  • Stars: 34
  • Watchers: 5
  • Forks: 23
  • Open Issues: 27
  • Releases: 12
Created almost 11 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog License

README.md

R/qtl2

R-CMD-check CRAN_Status_Badge zenodo DOI

Karl Broman

R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs.

Also see the related packages, qtl2convert (for converting data among the R/qtl2, DOQTL, and R/qtl formats), qtl2fst (for storing genotype probabilities on disk), and qtl2ggplot (for ggplot2-based data visualizations).

Installation

Install R/qtl2 from CRAN:

install.packages("qtl2")

Documentation

Citation

To cite R/qtl2 in publications, use:

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2019) R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations. Genetics 211:495-502 doi:10.1534/genetics.118.301595

License

Licensed under GPL-3.

Owner

  • Name: R/qtl
  • Login: rqtl
  • Kind: organization

GitHub Events

Total
  • Issues event: 6
  • Issue comment event: 3
  • Push event: 10
  • Fork event: 1
Last Year
  • Issues event: 6
  • Issue comment event: 3
  • Push event: 10
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 2,238
  • Total Committers: 4
  • Avg Commits per committer: 559.5
  • Development Distribution Score (DDS): 0.005
Past Year
  • Commits: 36
  • Committers: 1
  • Avg Commits per committer: 36.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Karl Broman k****n@g****m 2,227
Brian Yandell b****l@w****u 8
Karl Broman k****n@b****u 2
simecek l****a@g****m 1
Committer Domains (Top 20 + Academic)
biostat.wisc.edu: 1 wisc.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 99
  • Total pull requests: 20
  • Average time to close issues: 7 months
  • Average time to close pull requests: about 5 hours
  • Total issue authors: 12
  • Total pull request authors: 2
  • Average comments per issue: 0.82
  • Average comments per pull request: 0.1
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 1
  • Average time to close issues: about 7 hours
  • Average time to close pull requests: 1 day
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 1.25
  • 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
  • kbroman (87)
  • micwij (2)
  • BoraKim2018 (1)
  • kieranatkins (1)
  • gtsambos (1)
  • yifangt (1)
  • jamonterotena (1)
  • Jiseon623 (1)
  • rkmeade (1)
  • SmithLabDuke (1)
  • jeancarlier34 (1)
  • jlboat (1)
Pull Request Authors
  • kbroman (20)
  • byandell (2)
Top Labels
Issue Labels
bug (41) enhancement (29) documentation (10) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 886 last-month
  • Total docker downloads: 201
  • Total dependent packages: 7
  • Total dependent repositories: 10
  • Total versions: 9
  • Total maintainers: 1
cran.r-project.org: qtl2

Quantitative Trait Locus Mapping in Experimental Crosses

  • Versions: 9
  • Dependent Packages: 7
  • Dependent Repositories: 10
  • Downloads: 886 Last month
  • Docker Downloads: 201
Rankings
Forks count: 3.3%
Dependent packages count: 6.6%
Stargazers count: 8.6%
Dependent repos count: 9.2%
Average: 11.8%
Downloads: 17.3%
Docker downloads count: 25.8%
Maintainers (1)
broman@wisc.edu
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.1.0 depends
  • RSQLite * imports
  • Rcpp >= 1.0.7 imports
  • data.table >= 1.10.4 imports
  • grDevices * imports
  • graphics * imports
  • jsonlite >= 0.9.17 imports
  • parallel * imports
  • stats * imports
  • utils * imports
  • yaml >= 2.1.13 imports
  • devtools * suggests
  • qtl * suggests
  • roxygen2 * suggests
  • testthat * suggests
  • vdiffr * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite