rTASSEL
rTASSEL: An R interface to TASSEL for analyzing genomic diversity - Published in JOSS (2022)
Science Score: 95.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org -
✓Committers with academic emails
6 of 9 committers (66.7%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Repository
R front-end for TASSEL 5
Basic Info
- Host: GitHub
- Owner: maize-genetics
- License: apache-2.0
- Language: R
- Default Branch: master
- Homepage: https://rtassel.maizegenetics.net
- Size: 241 MB
Statistics
- Stars: 31
- Watchers: 2
- Forks: 9
- Open Issues: 0
- Releases: 8
Topics
Metadata Files
README.md
rTASSEL 
rTASSEL is an R-based front-end for accessing key TASSEL 5 methods and tools.
This allows users to run powerful TASSEL 5 analyses within a unified R workflow,
without switching between environments. rTASSEL also offers performance and
feature advantages over other R packages. See these benchmarks
for details.
Citation
To cite rTASSEL, please use the following citation:
Monier et al., (2022). rTASSEL: An R interface to TASSEL for analyzing genomic diversity. Journal of Open Source Software, 7(76), 4530, https://doi.org/10.21105/joss.04530
Installation
Stable release
```{r}
install.packages("pak")
pak::pak("maize-genetics/rTASSEL@v0.10.0") ```
Developmental version
```{r}
install.packages("pak")
pak::pak("maize-genetics/rTASSEL") ```
[!NOTE]
SincerTASSELusesrJava, you will need a working version of Java ($\geq$ 8).Mac/Linux users: you may need to run
R CMD javareconfif you run into issues with installingrJavaviapak. More installation tips can be found here.
Demo
If you want to test out what this package does but do not want to install it
locally, we have set up an interactive Jupyter notebook detailing the
walkthrough of rTASSEL on Binder. The Binder link can be accessed through
the Binder icon on this page or by clicking
here.
Getting help
For an overview of available functions, use the following command:
help(package = "rTASSEL")
If you need a walkthrough for potential pipelines, long-form documentation can be found on our website including a getting started article.
If you would like to study a function in full, refer to the R documentation
by using ?<function> in the console, where <function> is an
rTASSEL-based function.
Owner
- Name: Maize Genetics
- Login: maize-genetics
- Kind: organization
- Location: Cornell University, Ithaca, New York
- Website: https://www.maizegenetics.net/
- Repositories: 3
- Profile: https://github.com/maize-genetics
JOSS Publication
rTASSEL: An R interface to TASSEL for analyzing genomic diversity
Authors
Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853
Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853
Editor
Frederick Boehm
Tags
GWAS genetics genomic diversity genomic predictionGitHub Events
Total
- Create event: 3
- Release event: 1
- Issues event: 4
- Watch event: 3
- Delete event: 3
- Issue comment event: 3
- Push event: 22
- Pull request review comment event: 4
- Pull request review event: 5
- Pull request event: 2
Last Year
- Create event: 3
- Release event: 1
- Issues event: 4
- Watch event: 3
- Delete event: 3
- Issue comment event: 3
- Push event: 22
- Pull request review comment event: 4
- Pull request review event: 5
- Pull request event: 2
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Brandon | b****r@g****m | 569 |
| Edward Buckler | e****3@c****u | 45 |
| Unknown | a****s@g****m | 28 |
| Lynn Johnson | l****r@g****m | 13 |
| Sarah Jensen | s****5@c****u | 6 |
| ter56 | t****6@c****u | 4 |
| Travis Wrightsman | t****3@c****u | 4 |
| Terry Casstevens | t****6@c****u | 4 |
| Joe Gage | j****4@c****u | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 13
- Total pull requests: 4
- Average time to close issues: about 1 month
- Average time to close pull requests: about 3 hours
- Total issue authors: 8
- Total pull request authors: 2
- Average comments per issue: 1.46
- Average comments per pull request: 0.75
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 1
- Average time to close issues: 2 months
- Average time to close pull requests: about 10 hours
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 1.5
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tomsing1 (4)
- amelia-mendez (2)
- tkchafin (2)
- hidvegin (1)
- BB1464 (1)
- SabinaMT (1)
- robolvhez (1)
- snowformatics (1)
Pull Request Authors
- btmonier (3)
- danielskatz (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- GenomicRanges * imports
- IRanges * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- ape * imports
- ggplot2 * imports
- methods * imports
- rJava * imports
- rlang * imports
- BiocStyle * suggests
- knitr * suggests
- magrittr * suggests
- rmarkdown * suggests
- testthat * suggests
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- r-lib/actions/setup-r-dependencies v1 composite
- 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
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite