Gene Set Analysis Toolkit WebGestaltR

The web version WebGestalt < http://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 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 and Network Topology Analysis. The user-friendly output report allows 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 simultaneously analyze multiple gene lists.


WebGestalt R package is the R version of our well-known web application tool WebGestalt (www.webgestalt.org) that has on average 27,000 users from 140 countries and territories per year and has also been cited 371 in 2016. The advantage of this R package is that it can be easily integrated to other pipelines or simultaneously analyze multiple gene lists.

WebGestaltR function can perform popular enrichment analyses: ORA (Over-Representation Analysis), GSEA (Gene Set Enrichment Analysis) and NTA (Network Topology Analysis). Based on the user-uploaded gene list or gene list with scores (for GSEA method), WebGestaltR function will first map the gene list to entrez gene IDs and then summarize the gene list based on the GO (Gene Ontology) Slim data. After performing the enrichment analysis, WebGestaltR function also returns an user-friendly HTML report containing GO Slim summary and 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 0.4.0

20190422 —— Support of multiple databases for ORA and GSEA. Adjusted column names of the returned data frame.

WebGestalt 0.3.1

20190314 —— Bug fixes. The version with NAR update manuscript

WebGestalt 0.3.0

20190116 —— Major updates in HTML report and for 2019 publication

WebGestalt 0.1.1

Stable version in WebGestalt 2017 update

WebGestalt 0.0.1

20170207 —— First submit to CRAN

Reference manual

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install.packages("WebGestaltR")

0.4.1 by Yuxing Liao, 2 months ago


https://github.com/bzhanglab/WebGestaltR


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


Authors: Jing Wang [aut] , Yuxing Liao [aut, cre] , Eric Jaehnig [ctb] , Zhiao Shi [ctb] , Quanhu Sheng [ctb]


Documentation:   PDF Manual  


LGPL license


Imports methods, dplyr, doRNG, readr, parallel, doParallel, foreach, jsonlite, httr, rlang, igraph, whisker, apcluster, Rcpp

Linking to Rcpp

System requirements: C++11


See at CRAN