From db6b74d2fbb7c32d8d727d72cde9f69a18aa067d Mon Sep 17 00:00:00 2001 From: Guangchuang Yu Date: Thu, 6 Jun 2024 14:55:23 +0800 Subject: [PATCH] update --- contribution-knowledge-mining/index.html | 2 ++ 1 file changed, 2 insertions(+) diff --git a/contribution-knowledge-mining/index.html b/contribution-knowledge-mining/index.html index 0cebade..a8b33fe 100644 --- a/contribution-knowledge-mining/index.html +++ b/contribution-knowledge-mining/index.html @@ -292,10 +292,12 @@

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Users familiar with R/Bioconductor have several R packages to perform epigenomic enrichment analysis. ChIPseeker (Yu et al., 2015) provides a variety of functions for annotating user-provided ROIs in BED format by proximity to the nearby genes, finding overlaps with epigenomic regions, performing gene-centric and epigenomic enrichment analysis. ChIPseeker employs permutation strategy to calculate overlap enrichment p-values. ChIPseeker provides access to multi-organism epigenomic datasets from GEO (Gene Expression Omnibus), expanding enrichment analysis to species other than human. Coupled with excellent visualization capabilities, ChIPseeker is a well-designed tool with complete functionality for the interpretation of genome-wide ROIs.

– Excerpt from the article: Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning, Bioinformatics, 2017, 33(20):3323-3330.

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