EpiDiff: a computational tool for Epigenetic Difference Quantification and Identification by Entropy
  Summary Last Update: 03/12/2012

Welcome to EpiDiff!
EpiDiff (Epigenetic Difference Analysis Tool) is a quantitative tool, which is based on adapting Shannon entropy, for quantification of epigenetic difference and identification of genome regions differentially modified by epigenetic modifications or trans-acting factors. In addition, this tool also can be used to identify differentially expressed genes (DEGs).
Due to the different data format, three modules (QDCMR, QDMR, and QDEG) are provided for bioinformatic analysis of chromatin modifications data, DNA methylation data and gene expression data, respectively. The platform-free and species-free nature of EpiDiff makes it potentially applicable to various epigenetic data. This approach provides an effective tool for the high-throughput identification of the functional regions involved in epigenetic regulation.
The current version of EpiDiff provides users both Java Web Start and standalone software which is for huge dataset.
Each module of EpiDiff performs all of the steps including Import Data, Quantify Difference, Identify DCMRs/DMRs/DEGs, Measure Specificity and Export All Results. The modules can be turn to each other. Its graphical tools also allow the user to manually inspect the raw epigenetic data across samples any time.


  Getting Started   What's New More >>

Learn to use EpiDiff in 10 minutes:
Learn hands-on with the Quick Start tutorial

12/25/2011: EpiDiff 1.0 is now available. Run analysis via Java Web Start or download EpiDiff. This release includes support for Java 6. For more information, see the release notes. New!
Run analysis now via Java Web Start
Use EpiDiff to run analysis directly via Java Web Start.
12/22/2011: EpiDiff online tutorial is now available. And EpiDiff installers on different operating systems can be used formally.
Download EpiDiff
Use EpiDiff locally on Windows, Mac OS X, Linux, or Solaris.
12/21/2011: EpiDiff web server can be launched formally. And EpiDiff now provides UCSC link for each region to view genome information on UCSC database.

Please cite EpiDiff as you use it for your work:
EpiDiff: entropy-based quantitative identification of differential epigenetic modification regions from epigenomes

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