Master: Dev:

InterMine-R

R package for accessing InterMine instances

Installation

InterMineR has been added to Bioconductor.

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 errorinstallation 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.
  2. Comply with the standards of Bioconductor submission.
  3. Retrieve the available Mines from the InterMine registry.
• 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.

Stickers

Sticker templates are available from BiocStickers - or find us at a conference to pick some up in person.