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intermine/InterMineR

Name: InterMineR

Owner: InterMine

Description: R package for InterMine

Created: 2015-12-14 16:34:44.0

Updated: 2017-06-08 09:46:59.0

Pushed: 2017-11-21 11:39:20.0

Homepage: null

Size: 4177

Language: R

GitHub Committers

User	Most Recent Commit	# Commits
Julie Sullivan	2017-06-26 08:39:12.0	66
hpages	2017-10-30 16:54:32.0	2
Konstantinos Kyritsis	2018-03-02 13:25:16.0	472

Other Committers

User	Email	Most Recent Commit	# Commits
Samarth Mehrotra	f2015062@goa.bits-pilani.ac.in	2017-03-10 14:36:03.0	1

README

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

source("https://bioconductor.org/biocLite.R")

biocLite("InterMineR")

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

License

LGPL. See LICENSE for details.

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.