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Enrichment analysis with EpiAnnotator

Enrichment analysis with EpiAnnotator MotivationDeciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way.ResultsEpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures.Availability and implementationThe R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator’s web interface is accessible at http://computational-epigenomics.com/en/epiannotator. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

Enrichment analysis with EpiAnnotator

Pageaud, Yoann; Plass, Christoph; Assenov, Yassen
Bioinformatics , Volume 34 (10): 3 – Jan 10, 2018
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Publisher
Oxford University Press
Copyright
© The Author(s) 2018. Published by Oxford University Press.
ISSN
1367-4803
eISSN
1460-2059
DOI
10.1093/bioinformatics/bty007
Publisher site
See Article on Publisher Site

Abstract

MotivationDeciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way.ResultsEpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures.Availability and implementationThe R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator’s web interface is accessible at http://computational-epigenomics.com/en/epiannotator.

Journal

Bioinformatics – Oxford University Press

Published: Jan 10, 2018

References

  • genomation: a toolkit to summarize, annotate and visualize genomic intervals
    Akalin, A.
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    Albrecht, F.
  • The NIH Roadmap Epigenomics Mapping Consortium
    Bernstein, B.E.
  • The International Human Epigenome Consortium Data Portal
    Bujold, D.
  • The ENCODE (ENCyclopedia of DNA elements) project
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    Halachev, K.
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    Huang, D.W.
  • The UCSC genome browser database
    Karolchik, D.
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    Lawrence, M.
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    Sheffield, N.C.; Bock, C.
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