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
- Fork it!
- Create your feature branch:
git checkout -b my-new-feature
- Commit your changes:
git commit -am 'Add some feature'
- Push to the branch:
git push origin my-new-feature
- 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:
- Operate with the InterMine web services.
- Comply with the standards of Bioconductor submission.
- 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:
simplifyResult
function for flattened results display.
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.