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R package for WebGestalt
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inst Expose parameter p for GSEA Dec 9, 2019
man Expose parameter p for GSEA Dec 9, 2019
src Adjust not to multiply expression values when set total score sums to… Dec 6, 2018
.gitignore Extract and refactor codes of HTML output to use template. Mar 20, 2018
NAMESPACE Add option to ouput GSEA enrichment in SVG. Sep 25, 2019 Update changelog Sep 16, 2019 Close #2. Add cache option to reuse server data. May 20, 2019

WebGestalt R package is the R version of our well-known web application tool WebGestalt ( 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.

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