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Software for motif discovery and next generation sequencing analysis



HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.

Hardware Requirements (recommended): 2+ Gb memory (4-8+ Gb), 10+ Gb Hard Drive space (50+ Gb)
Software Requirements: Unix compatible OS (or cygwin), perl, gcc, make, wget (optional for full functionality: R, DESeq2, blat, bedGraphToBigWig, liftOver)
License: GPLv3

HOMER works on pretty much any Linux/UNIX systems, including MacOS (if Xcode compilers are installed) and on Windows using either cygwin or a Linux subsystem.

If you are looking specifically for HOMER2, you are in the right place! HOMER2 is integrated into HOMER.

Full Program Download

Jetbrainsresettrial | [top]

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Students and educators at accredited institutions can apply for a covering All Products Packs. This program requires validation via an active university email address ( .edu ) or an official International Student Identity Card (ISIC). Open-Source Project Support

: Lead developers of non-commercial open-source projects can apply for free licenses. Startup Discounts jetbrainsresettrial

If you need further assistance with your development environment, let me know:

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It is a widely searched term among developers, often leading to repositories on GitHub, scripts on forums, or "cracked" versions of software. But what exactly does this process do, how does it work, and what are the risks involved?

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Which (e.g., IntelliJ, PyCharm, WebStorm) are you currently evaluating? Do you hold any student or academic credentials ? Relying on these workarounds poses significant risks to

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The trial version is identical to the paid professional version, ensuring you can test every advanced feature before purchasing. The Risks of "Reset Trial" Scripts and Workarounds

Program Components and Older Versions

homer2 program - key executable for HOMER motif discovery (homerCppOnly.*.zip). (This archive actually contains all of the c++ executable, not just homer2).  Unzip in the desired directory and simply type "make" to compile the program.

The configuration script really doesn't deal with older versions, but you can download older versions yourself should you really feel like using inferior data or software!
Old Versions of HOMER Software
Old Versions of Organism Packages
Old Versions of Promoter Packages
Old Versions of Genome Packages

Update Information

Change Log - Short description of recent changes

update.txt - Current HOMER configuration list (Currently support human hg17/hg18/hg19, mouse mm8/mm9, rat rn4, X. tropicalis xenTro2, drosophila dm3, and C. elegans ce6, Zebrafish danRer7, yeast sacCer2, Arabidopsis tair10, Rice msu6, Pombe ASM294v1)


jetbrainsresettrial
Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@ucsd.edu