https://github.com/intermine/interminer
R package for InterMine
https://github.com/intermine/interminer
biology genomics intermine r
Last synced: 6 months ago
JSON representation
R package for InterMine
- Host: GitHub
- URL: https://github.com/intermine/interminer
- Owner: intermine
- License: lgpl-2.1
- Created: 2015-12-14T16:34:44.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2022-04-05T14:19:21.000Z (almost 4 years ago)
- Last Synced: 2025-06-11T01:41:31.585Z (7 months ago)
- Topics: biology, genomics, intermine, r
- Language: R
- Size: 8.33 MB
- Stars: 18
- Watchers: 10
- Forks: 16
- Open Issues: 19
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Master: [![Build Status: master][travis-badge-master]][ci] Dev: [![Build Status: dev][travis-badge-dev]][ci]
# InterMine-R
R package for accessing InterMine instances
## Installation
InterMineR has been added to [Bioconductor](https://bioconductor.org/packages/release/bioc/html/InterMineR.html).
To install this package, start R and enter:
`## try http:// if https:// URLs are not supported`
`if (!requireNamespace("BiocManager", quietly=TRUE))`
`install.packages("BiocManager")`
`BiocManager::install("InterMineR")`
In case installation for RCurl fails showing the error`installation of package ‘RCurl’ had non-zero exit status`, install libxml2-dev, libcurl4-openssl-dev and aptitude on you system using the following commands :
`sudo apt-get install aptitude`
`sudo apt-get install libcurl4-openssl-dev`
`sudo apt-get install libxml2-dev`
## Usage
See HTML vignettes for detailed API and tutorials:
* vignettes/InterMineR.Rmd
* vignettes/Enrichment_Analysis_and_Visualization.Rmd
* vignettes/FlyMine_Genomic_Visualizations.Rmd
## Contributing
1. Fork it!
2. Create your feature branch: `git checkout -b my-new-feature`
3. Commit your changes: `git commit -am 'Add some feature'`
4. Push to the branch: `git push origin my-new-feature`
5. Submit a pull request :D
## Credits
Bing Wang:
* InterMineR package creation (first edition)
* Established the first query system (queries as list objects)
* Vignette creation (first edition)
Konstantinos Kyritsis:
* InterMineR package update to:
1. Operate with the [InterMine web services](http://intermine.readthedocs.io/en/latest/web-services/).
2. Comply with the standards of [Bioconductor submission](https://www.bioconductor.org/developers/package-submission/).
3. Retrieve the available Mines from the [InterMine registry](http://registry.intermine.org/).
* Established the second query system (queries as `InterMineR-class` objects)
* Addition of enrichment analysis functionality and convertion of the results to `GeneAnswer-class` objects
* Addition of functionality for converting InterMineR-retrieved data to `GRanges-class` and `RangedSummarizedExperiment-class` objects
* Additional functions:
1. `simplifyResult` function for flattened results display.
2. `listDatasets` and `getDatasets` to retrieve information about the available datasets in each Mine.
* Vignette update (second edition)
* Addition of tutorials for *Enrichment Analysis and Visualization* and *FlyMine Genomic Visualizations* with InterMineR
Celia Sanchez Laorden
* Created the listManager class for dealing with lists of objects within InterMineR
* Created methods get_list, delete_listand create_list
* Created functions intersect, union, difference and subtract.
* Created auxiliary methods: GET_api_list which returns the response object of the Request, get_unused_list_name which checks if the name given by the
user has been already used and, in such a case, provides a new one, and do_operation which creates a new list results of an operation.
## License
LGPL. See LICENSE for details.
[travis-badge-master]: https://travis-ci.org/intermine/InterMineR.svg?branch=master
[ci]: https://travis-ci.org/intermine/InterMineR
[travis-badge-dev]: https://travis-ci.org/intermine/InterMineR.svg?branch=dev
## Stickers
Sticker templates are available from [BiocStickers](https://github.com/Bioconductor/BiocStickers/tree/master/InterMineR) - or find us at a conference to pick some up in person.