Science Score: 46.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
5 of 19 committers (26.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary
Keywords from Contributors
Repository
R/qtl: A QTL mapping environment
Basic Info
- Host: GitHub
- Owner: kbroman
- License: gpl-3.0
- Language: R
- Default Branch: main
- Homepage: https://rqtl.org
- Size: 21.2 MB
Statistics
- Stars: 85
- Watchers: 9
- Forks: 46
- Open Issues: 5
- Releases: 10
Metadata Files
README.md
R/qtl: A QTL mapping environment
Authors: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Śaunak Sen and contributions from Danny Arends, Robert Corty, Timothée Flutre, Ritsert Jansen, Pjotr Prins, Lars Rönnegård, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses. It is implemented as an add-on package for the freely available and widely used statistical language/software R. The development of this software as an add-on to R allows us to take advantage of the basic mathematical and statistical functions, and powerful graphics capabilities, that are provided with R. Further, the user will benefit by the seamless integration of the QTL mapping software into a general statistical analysis program. Our goal is to make complex QTL mapping methods widely accessible and allow users to focus on modeling rather than computing.
A key component of computational methods for QTL mapping is the hidden Markov model (HMM) technology for dealing with missing genotype data. We have implemented the main HMM algorithms, with allowance for the presence of genotyping errors, for backcrosses, intercrosses, and phase-known four-way crosses.
The current version of R/qtl includes facilities for estimating genetic maps, identifying genotyping errors, and performing single-QTL genome scans and two-QTL, two-dimensional genome scans, by interval mapping (with the EM algorithm), Haley-Knott regression, and multiple imputation. All of this may be done in the presence of covariates (such as sex, age or treatment). One may also fit higher-order QTL models by multiple imputation and Haley-Knott regression.
License
The R/qtl package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.
A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3
Owner
- Name: Karl Broman
- Login: kbroman
- Kind: user
- Location: Madison, Wisconsin, USA
- Company: University of Wisconsin-Madison
- Website: https://kbroman.org
- Repositories: 412
- Profile: https://github.com/kbroman
Professor in Dept of Biostatistics & Medical Informatics at UW–Madison. Applied statistician working on statistical genomics.
GitHub Events
Total
- Issues event: 4
- Watch event: 9
- Issue comment event: 4
- Fork event: 1
Last Year
- Issues event: 4
- Watch event: 9
- Issue comment event: 4
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Karl Broman | k****n@g****m | 1,192 |
| DannyArends | D****s@g****m | 613 |
| Pjotr Prins | p****1@t****l | 441 |
| DannyArends | d****s@g****m | 182 |
| kbroman | k****n@2****3 | 136 |
| Karl Broman | k****n@b****u | 106 |
| DannyArends | D****s@G****m | 31 |
| Brian S. Yandell | b****l@w****u | 27 |
| aaronwolen | a****n@w****m | 26 |
| unknown | D****s@r****l | 11 |
| Robert Corty | r****y@g****m | 7 |
| Rohan Shah | r****h@u****t | 3 |
| Quoc | t****c@g****m | 2 |
| Timothée Flutre | t****e@g****m | 2 |
| Timothée Flutre | t****e@i****r | 2 |
| (no author) | (****)@2****3 | 1 |
| Alex Whan | a****n@g****m | 1 |
| Quoc Tran | t****n@s****u | 1 |
| unknown | t****n@b****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 71
- Total pull requests: 39
- Average time to close issues: 3 months
- Average time to close pull requests: 7 days
- Total issue authors: 16
- Total pull request authors: 8
- Average comments per issue: 1.61
- Average comments per pull request: 0.9
- Merged pull requests: 22
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: about 1 hour
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kbroman (46)
- timflutre (4)
- pcarbo (4)
- xiekunwhy (3)
- ytguojian (2)
- jcberny (2)
- huangl07 (1)
- webbchen (1)
- ellert (1)
- jtlovell (1)
- shaito9 (1)
- DivijaGaniga (1)
- fdchevalier (1)
- jeancarlier34 (1)
- jingxianyu (1)
Pull Request Authors
- rcorty (12)
- DannyArends (11)
- kbroman (5)
- timflutre (5)
- rohan-shah (2)
- QuocTran (2)
- aaronwolen (2)
- alexwhan (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 2,961 last-month
- Total docker downloads: 43,887
- Total dependent packages: 35
- Total dependent repositories: 80
- Total versions: 74
- Total maintainers: 1
cran.r-project.org: qtl
Tools for Analyzing QTL Experiments
- Homepage: https://rqtl.org
- Documentation: http://cran.r-project.org/web/packages/qtl/qtl.pdf
- License: GPL-3
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Latest release: 1.70
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 2.14.0 depends
- grDevices * imports
- graphics * imports
- parallel * imports
- stats * imports
- utils * imports
- testthat * suggests
- 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
- r-lib/actions/setup-tinytex v2 composite