Skip to content

Latest commit

 

History

History
88 lines (57 loc) · 3.51 KB

README.md

File metadata and controls

88 lines (57 loc) · 3.51 KB
Raw

Master: Build Status: master Dev: Build Status: 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.