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About EpiCenter

EpiCenter is a powerful analysis tool of genome-wide mRNA-seq or ChIP-seq data for detecting differentially expressed genes or identifying changes in epigenetic modifications (histone acetylation/methylation patterns). EpiCenter is also capable of performing genome-wide TFBS peaking detection and generating read coverage depth plot data (e.g., WIG files for UCSC genome browser). Implemented with C++ language, EpiCenter is efficient, and typically requires less than 10 minutes to analyze a large dataset. EpiCenter supports major read alignment formats including SAM, BAM, ELAND export, and MAQ formats.

What's New

• the version 1-6-1-8 was released on 06/13/2011
• gene annotation files of four species for EpiCenter are now available here
• analysis examples of both ChIP-seq and mRNA-seq data can be downloaded here
• the version 1-5-9-8 was released on 03/15/2011
• the version 1-5-8-8 was released on 12/30/2010
• EpiCenter is also available at its NIH mirror site

Availability

EpiCenter is freely available to the public. The binary packages of EpiCenter are available for all three major operating systems: Linux, Macintosh, and Windows, and can be downloaded at the following links. The C++ source code is also available upon request for advanced users.

NOTE: please install and use a 64-bit version program if you have 64-bit operating system. 32 bit packages are for the 32-bit operating system and you may be not able to use it to analyze very large datasets if more than 4GB memory is required for the analysis.

Version 1-6-1-8 (Latest Version)

	Linux packages	MacOS X packages	Windows packages
64-bit system	epicenter_Linux64.tar.gz	epicenter_MacOS64.tar.gz	epicenter_Win64.zip
32-bit system	epicenter_Linux32.tar.gz	epicenter_MacOS32.tar.gz	epicenter_Win32.zip

Version 1-5-9-8

	Linux packages	MacOS X packages	Windows packages
64-bit system	epicenter_Linux64.tar.gz	epicenter_MacOS64.tar.gz	epicenter_Win64.zip
32-bit system	epicenter_Linux32.tar.gz	epicenter_MacOS32.tar.gz	epicenter_Win32.zip

Version 1-5-8-8

	Linux packages	MacOS X packages	Windows packages
64-bit system	epicenter_Linux64.tar.gz	epicenter_MacOS64.tar.gz	epicenter_Win64.zip
32-bit system	epicenter_Linux32.tar.gz	epicenter_MacOS32.tar.gz	epicenter_Win32.zip

Version 1-5-7-8

	Linux packages	MacOS X packages	Windows packages
64-bit system	epicenter_Linux64.tar.gz	epicenter_MacOS64.tar.gz	epicenter_Win64.zip
32-bit system	epicenter_Linux32.tar.gz	epicenter_MacOS32.tar.gz	epicenter_Win32.zip

Installation

Recommended hardware requirements

• CPU: 1GHZ or higher
• Memory: 4GB or more
• Disk space: 100 GB or more

Installation

Installation is to simply decompress one of the above EpiCenter compressed packages to your installation location.

Linux or MacOS X

If you download the package epicenter_<OS>.tar.gz to the folder "/home/<username>/downloads", and then you can issue the following commands to install the program to the folder "/home/<username>/install_dir" at your terminal window:

• cd /home/<username>/install_dir
• tar xfz /home/<username>/downloads/epicenter_<OS>.tar.gz
• cd epicenterDIR
• if needed, run ./install.sh to copy main executable binary files into "/home/<username>/bin"

Windows

EpiCenter's packages are in ZIP packages. Installation is simply to extract the package to a desired installation location. After extraction, open the extracted folder "epicenterDIR". Then double click the window batch file "launch_epicenter.bat" to launch Windows' Command Line Terminal, where you can run EpiCenter programs.

All programs and documents will be in the folder install_dir/epicenterDIR.

Usages and Documents

• Usage (type 0-3, 31, 32) for Genome-wide comparison analysis of two samples

          ./EpiCenter -t analysis_type [options] –i aln_type aln_sample1 aln_sample2

• Usage (type 4) for read coverage analysis of a single sample

          ./EpiCenter -t 4 [options] –i aln_type aln_sample

• Usage (type 5) for converting ChIP/mRNA-seq data files into a data matrix

          ./EpiCenter -t 5 -f genomic_LOC_info_file [options] –i aln_type aln_file1 [aln_file2 ...]

For details of usages, please refer to the following EpiCenter user manual

• PDF user manual

Supplemental data and application examples

Gene annotation files of four popular species for research studies

• the human genome (hg19 knownGene) [1.1M]
• the mouse genome (mm9 refGene) [380K]
• the D. melanogaster genome (flybase version r5.31, RA isoforms only) [272K]
• the Pombe yeast genome (Sanger 01-29-2010) [380K]

Examples

1. Detecting epigenetic changes with histone ChIP-seq data
   • analysis program codes [1.8M]
   • read alignment E14_10dEB.map [413M]
   • read alignment E14_undiff.map [259M]
   • read alignment LF2_10dEB.map [401M]
   • read alignment LF2_undiff.map [284M]
   
   
2. Identifying differentially expressed genes with mRNA-seq data
   • analysis program codes [1.5M]
   • read alignment Dmel_male.map [604M]
   • read alignment Dmel_female.map [686M]

Contact Author

Weichun Huang at Biostatistics Branch, the National Institute of Environmental Health Sciences (NIEHS), NIH

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Copyright© 2009-2011 Weichun Huang