EpiAnnotator - Help & Discussions Thread
Welcome to the EpiAnnotator thread !
Table of Contents
- What is EpiAnnotator?
- Why did we create EpiAnnotator?
- How does EpiAnnotator work
- Tutorials and Documentation
- Frequent Errors
- Contact
- Reference Paper
What is EpiAnnotator?
EpiAnnotator is a free web service developed by the Computational Epigenomics team at DKFZ, Heidelberg allowing researchers from all around the world to decipher relevant biological insights from their own (epi)genomic data.
An Enrichment Analysis is based on 2 BED files (storing your selected and backgroung genomic regions) and annotations you select from the interface. EpiAnnotator can then compute the overlaps between genomic regions from your files and the ones from the selected annotation. Results are typically returned in few seconds. Finally, you can export a table with all results and elegant summary plots, ready for your lab presentation or publication.
Why did we create EpiAnnotator?
With EpiAnnotator we wanted to ensure an access to the latest versions of thousands of annotations coming from useful repositories (ENCODE, the UCSC Genome Browser, the International Human Epigenome Consortium, ...) for every scientist working in the field of genomics. Using EpiAnnotator doesn’t require any coding skills or any special IT infrastructure. All you need is a computer, your data and an Internet connection.
How does EpiAnnotator work?
EpiAnnotator uses Fisher’s Exact Test to determine if there is an enrichment or depletion for your genomic regions on the annotations of interest. It also calculates the fold change and the p value associated with the overlaps in order to determine significance levels.
Tutorials and Documentation
- How to use EpiAnnotator
- How to install a local copy of EpiAnnotator
- How annotations are stored in EpiAnnotator
Frequent Errors
(Frequent Errors Help will be added soon!)
If this section did not helped you, feel free to leave your comments & questions below!
Contact
If you are experiencing errors, or observing an unexpected behavior of EpiAnnotator, please report it below in a comment. Alternatively, you can send us an email to: epiannotator@computational-epigenomics.com
Reference Paper
Pageaud Y., Plass C., Assenov Y. (2018) *Enrichment Analysis with EpiAnnotators. Bioinformatics.*
