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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

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Program Components and Older Versions

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: To find high-quality files, users often include specific video extensions like .mkv , .mp4 , or .avi in their search string.

Users often find these directories by using specific search queries, known as "Google Dorks," parent directory index hollywood movies link

While using a "parent directory index hollywood movies link" may seem like an appealing option, it's essential to understand the risks and consequences associated with it. Here are some of the potential dangers: : To find high-quality files, users often include

Parent Directory Action/ Comedy/ Sci-Fi/ The_Matrix_1999.mp4 Inception_2010.mkv Titanic_1997.mp4 : To find high-quality files

Never download a file that ends in .exe , .zip , or .scr if you are looking for a movie.


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