epiSeeker

Description

This package implements functions to analyze multi-omics epigenetic data. Data of fragment type and base type are supported by epiSeeker. It provides functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statistical methods to estimate the significance of overlap among peak data sets, and motif analysis. It incorporates the GEO database for users to compare their own dataset with those deposited in the database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, overlap of peaks or genes, and the single-base resolution epigenetic data by considering the strand, motif, and additional information.

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People

• Guangchuang Yu author maintainer fnd
• Chun-Hui Gao contributor
• Michael Kluge contributor
• Ming Li contributor
• Hervé Pagès contributor
• Thomas Schwarzl contributor
• Qianwen Wang contributor
• Zhougeng Xu contributor
• Yun Yan contributor