The R Version of WebGestalt

The web version WebGestalt < http://www.webgestalt.org> supports 12 organisms, 324 gene identifiers and 150,937 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis. The user-friendly output interface allow interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneous analyze multiple gene lists.


WebGestalt R package is the R version of our well-known web application tool WebGestalt (www.webgestalt.org) that has been visited 57,880 times by 26,233 users from 140 countries and territories in 2016 and has also been cited 371 in 2016. The advantage of this R package is it can be easily integrated to other pipeline or simultaneous analyze multiple gene lists.

WebGestalt function can perform two popular enrichment analyses: ORA (Over-Representation Analysis) and GSEA (Gene Set Enrichment Analysis). Based on the user uploaded gene list or gene list with scores (for GSEA method), WebGestalt function will first map the gene list to the entrez gene ids and then summary the gene list based on the GO (Gene Ontology) Slim. After performing the enrichment analysis, WebGestalt function also returns an user-friendly HTML report containing the ID mapping table, GO Slim summary result and the enrichment analysis result. If the functional categories have the DAG (directed acyclic graph) structure, the structure of the enriched categories can also be visualized in the report.

News

WebGestalt 0.0.1

20170207 —— First submit to CRAN

Reference manual

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install.packages("WebGestaltR")

0.1.1 by Jing Wang, 9 months ago


Browse source code at https://github.com/cran/WebGestaltR


Authors: Jing Wang <[email protected]>


Documentation:   PDF Manual  


LGPL license


Imports methods, data.table, parallel, doParallel, foreach, PythonInR, pkgmaker, rjson

System requirements: Java, Python


See at CRAN