EpiDiff: a computational tool for Epigenetic Difference Quantification and Identification by Entropy
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Tutorials for Individual Modules
Tutorial for 1

 
Tutorial for 3
Tutorial for 2
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EpiDiff provides a quantitative approach to quantify difference and identify DCMRs, DMRs and DEGs from genome-wide epigenetic and expression profiles by adapting Shannon entropy. Its platform-free and species-free nature makes it easy for computational biologists to analysis the epigenetic regulation across various temporal and spatial epigenomes.

This Tutorial contains the following sections:
Getting Started Describes how to start Local and online EpiDiff.
Tutorial for three modules Describes how to use three modules in EpiDiff.
Getting Started ^Tutorial ^Top
This section describes how to start online and local EpiDiff.

Before start QDCMR, user should start EpiDiff using two ways:
1. Start EpiDiff directly via Java Web Start, using the Java Web Start feature (advantage: no installation required);
2. Download EpiDiff installation package, install and run it locally on your machine (advantage: no network required).

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And then, click one the button "Other Services" to change to QDEG service in the following picture.

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Tutorial for three modules ^Tutorial ^Top
There are three modules in EpiDiff. The detail Tutorial is provided single-handedly. Please look for the Tutorial by click the icon for each modules.
Tutorial for  
Tutorial for
Tutorial for
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1. Public Server/General
  1) What is the latest version of EpiDiff?
  A. The latest version of EpiDiff is 1.0 (Release Note). With the increased functionality, we will develop the later EpiDiff.
  2) Where can I find the hardware and software prerequisites for EpiDiff?
  A. The hardware requirements, supported operating systems, and supported browsers is shown in Download site.
  3) How can I get help with EpiDiff or provide feedback?
  A. The tutorial fully describes QDMR and how to use it.
To provide feedback or ask a question please do not hesitate to contact Hongbo Liu (hongbo919@gmail.com) or Yan Zhang (yanyou1225@yahoo.com.cn).

2. Installation
  1) How do I install (uninstall) EpiDiff?
  A. To install EpiDiff, go to EpiDiff Download to download the EpiDiff for your operating system. Then install EpiDiff by double-clicking or decompressing.
To uninstall EpiDiff, use the utility provided as part of the EpiDiff installation. If the EpiDiff uninstall utility is unavailable, delete the EpiDiff installation folder and remove all EpiDiff files other than the desktop icons.
  2) Is the source code available?
  A. Yes. Source code for EpiDiff is available under the EpiDiff software license. For access to the source code, email the EpiDiff team.

3.Data Formats
  1) What file format dose EpiDiff support?
  A. For different module, EpiDiff support different file format which can be found in the Tutorial for three modules.

4.Other
If you have any trouble or recommendations, please do not hesitate to contact Hongbo Liu (hongbo919@gmail.com) or Yan Zhang (yanyou1225@yahoo.com.cn).
Our Lab:Group of computational epigenetic research
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College of Bioinformatics Science and Technology, Harbin Medical University, China
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