Master: [![Build Status: master][travis-badge-master]][ci] Dev: [![Build Status: dev][travis-badge-dev]][ci] # InterMine-R <img src="https://cdn.rawgit.com/Bioconductor/BiocStickers/e3a0fb08/InterMineR/InterMineR.png" width="200" /> 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.