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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

: For very long posts, a clickable table of contents helps readers navigate quickly [7].

: End your post by asking readers to leave a comment or share the post on social media [7, 8].

What is the of the images (e.g., travel, a wedding, a technical tutorial)? Who is your target audience ?

: Link to other posts on your site and reputable external sources to build authority [1, 8]. 🖼️ Phase 3: Optimizing Your Images

Program Components and Older Versions

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: For very long posts, a clickable table of contents helps readers navigate quickly [7].

: End your post by asking readers to leave a comment or share the post on social media [7, 8]. IMG_2500.rar

What is the of the images (e.g., travel, a wedding, a technical tutorial)? Who is your target audience ? : For very long posts, a clickable table

: Link to other posts on your site and reputable external sources to build authority [1, 8]. 🖼️ Phase 3: Optimizing Your Images : For very long posts

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)

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