qtl2pleio

multiparental-populations quantitative-genetics quantitative-trait

Score: 10.154401900795694

Last synced: about 7 hours ago
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Repository metadata:

Testing pleiotropy vs. separate QTL in multiparental populations

Host: GitHub
URL: https://github.com/fboehm/qtl2pleio
Owner: fboehm
License: other
Created: 2017-09-22T16:06:34.000Z (over 8 years ago)
Default Branch: master
Last Pushed: 2026-05-29T13:12:15.000Z (25 days ago)
Last Synced: 2026-06-11T18:03:55.430Z (12 days ago)
Topics: multiparental-populations, quantitative-genetics, quantitative-trait
Language: R
Homepage:
Size: 5.25 MB
Stars: 6
Watchers: 2
Forks: 2
Open Issues: 11
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- License: LICENSE
- Codemeta: codemeta.json
- Zenodo: .zenodo.json

CodeMeta metadata:

@context: https://doi.org/10.5063/schema/codemeta-2.0
@type: SoftwareSourceCode
Identifier: qtl2pleio
Description: We implement an adaptation of Jiang & Zeng's (1995) likelihood ratio test for testing the null hypothesis of pleiotropy against the alternative hypothesis, two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995) and that in Tian et al. (2016) in that our test accommodates multiparental populations.
Name: qtl2pleio: Testing Pleiotropy in Multiparental Populations
Code repository: https://github.com/fboehm/qtl2pleio
Issue tracker: https://github.com/fboehm/qtl2pleio/issues
License: https://spdx.org/licenses/MIT
Version: 1.4.4
Programming language:
- @type: ComputerLanguage
- Name: R
- Url: https://r-project.org
Runtime platform: R version 4.5.2 (2025-10-31)
Provider:
- @id: https://cran.r-project.org
- @type: Organization
- Name: Comprehensive R Archive Network (CRAN)
- Url: https://cran.r-project.org
Author:
- - @type: Person
  - Given name: Frederick J
  - Family name: Boehm
  - Email: frederick.boehm@gmail.com
  - @id: https://orcid.org/0000-0002-1644-5931
Maintainer:
- - @type: Person
  - Given name: Frederick J
  - Family name: Boehm
  - Email: frederick.boehm@gmail.com
  - @id: https://orcid.org/0000-0002-1644-5931
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File size: 99175.901KB
Citation:
- - @type: ScholarlyArticle
  - Date published: 2019
  - Author:
    - - @type: Person
      - Given name:
        Frederick
        J.
      - Family name: Boehm
    - - @type: Person
      - Given name:
        Elissa
        J.
      - Family name: Chesler
    - - @type: Person
      - Given name:
        Brian
        S.
      - Family name: Yandell
    - - @type: Person
      - Given name:
        Karl
        W.
      - Family name: Broman
  - Name: Testing pleiotropy vs. separate QTL in multiparental populations
  - Identifier: 10.1093/genetics/140.3.1111
  - Url: https://doi.org/10.1534/g3.119.400098
  - Pagination: 2317-2324
  - @id: https://doi.org/10.1093/genetics/140.3.1111
  - Same as: https://doi.org/10.1093/genetics/140.3.1111
  - Is part of:
    - @type: PublicationIssue
    - Date published: 2019
    - Is part of:
      - @type:
        PublicationVolume
        Periodical
      - Volume number: 9
      - Name: G3
Release notes: https://github.com/fboehm/qtl2pleio/blob/main/NEWS.md
Readme: https://github.com/fboehm/qtl2pleio/blob/master/README.md
Cont integration:
- https://github.com/fboehm/qtl2pleio/actions
- https://app.codecov.io/github/fboehm/qtl2pleio?branch=master
Development status: https://www.repostatus.org/#active
Keywords:
- quantitative-trait
- quantitative-genetics
- multiparental-populations
Related link: https://CRAN.R-project.org/package=qtl2pleio

Owner metadata:

Name: Frederick Boehm
Login: fboehm
Email: frederick.boehm@gmail.com
Kind: user
Description: I study biostatistics, with a focus in statistical genetics. I strive to understand how our genes influence our health and biology.
Website: https://fboehm.us/
Location: Brookings, South Dakota, USA
Twitter:
Company: South Dakota State University
Icon url: https://avatars.githubusercontent.com/u/4155196?u=2ced538fd395d36c43a81f1ed5cdeb5b6f6bdf60&v=4
Repositories: 242
Last Synced at: 2026-04-22T19:38:31.454Z
Profile URL: https://github.com/fboehm

GitHub Events

Total

Issue comment event: 1
Pull request event: 1
Push event: 2
Total: 4

Last Year

Issue comment event: 1
Pull request event: 1
Push event: 2
Total: 4

Committers metadata

Last synced: about 2 months ago

Total Commits: 644
Total Committers: 3
Avg Commits per committer: 214.667
Development Distribution Score (DDS): 0.02

Commits in past year: 9
Committers in past year: 2
Avg Commits per committer in past year: 4.5
Development Distribution Score (DDS) in past year: 0.444

Name	Email	Commits
Frederick Boehm	f**m@g**m	631
Karl Broman	k**n@g**m	12
Kyle Niemeyer	k**r@g**m	1

Issue and Pull Request metadata

Last synced: 4 months ago

Total issues: 43
Total pull requests: 3
Average time to close issues: about 1 month
Average time to close pull requests: 26 minutes
Total issue authors: 2
Total pull request authors: 2
Average comments per issue: 1.28
Average comments per pull request: 1.0
Merged pull request: 3
Bot issues: 0
Bot pull requests: 0

Past year issues: 0
Past year pull requests: 0
Past year average time to close issues: N/A
Past year average time to close pull requests: N/A
Past year issue authors: 0
Past year pull request authors: 0
Past year average comments per issue: 0
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/fboehm/qtl2pleio

Top Issue Authors

fboehm (39)
HongHe0123 (4)

Top Pull Request Authors

kbroman (2)
kyleniemeyer (1)

Top Issue Labels

enhancement (10)
bug (5)
good first issue (4)

Top Pull Request Labels

Package metadata

Total packages: 1
Total downloads:
- cran: 503 last-month
Total dependent packages: 0
Total dependent repositories: 0
Total versions: 5
Total maintainers: 1

cran.r-project.org: qtl2pleio

Testing Pleiotropy in Multiparental Populations

Homepage: https://github.com/fboehm/qtl2pleio
Documentation: http://cran.r-project.org/web/packages/qtl2pleio/qtl2pleio.pdf
Licenses: MIT + file LICENSE
Latest release: 1.4.4 (published about 2 months ago)
Last Synced: 2026-06-03T03:32:06.611Z (20 days ago)
Versions: 5
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 503 Last month
Rankings:
- Forks count: 21.888%
- Stargazers count: 24.172%
- Dependent packages count: 29.797%
- Average: 34.197%
- Dependent repos count: 35.455%
- Downloads: 59.674%
Maintainers (1)
- frederick.boehm@gmail.com

Dependencies

DESCRIPTION cran

R >= 3.2 depends
MASS * imports
Rcpp * imports
dplyr * imports
gemma2 * imports
ggplot2 * imports
magrittr * imports
parallel * imports
rlang * imports
tibble * imports
broman * suggests
covr * suggests
devtools * suggests
knitr * suggests
mvtnorm * suggests
parallelly * suggests
qtl2 * suggests
rmarkdown * suggests
testthat * suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Summary