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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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: The film was a major success, grossing $235 million and earning two Golden Globe nominations , including Best Motion Picture – Musical or Comedy. Unrated vs. Theatrical Differences

: While McCarthy is the lead, Jason Statham received widespread praise for a self-aware, comedic performance as Rick Ford , a hyper-macho but incompetent agent. : The film was a major success, grossing

The Unrated/Extended Cut (130 minutes) offers several variations over the 120-minute theatrical version: Movie Highlights

: After field agent Bradley Fine ( Jude Law ) is assassinated by arms dealer Rayna Boyanov ( Rose Byrne ), Susan Cooper volunteers to go deep undercover to infiltrate Rayna's circle and prevent a global crisis. directed by Paul Feig

The 2015 action-comedy , directed by Paul Feig , follows CIA desk analyst Susan Cooper (played by Melissa McCarthy ) as she unexpectedly transitions to field duty to track a stolen nuclear device after her partner is compromised. The "Unrated" version typically found on Blu-ray includes approximately 10 minutes of extra footage , consisting of extended scenes, more improv gags, and increased profanity or crude humor. Movie Highlights

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)

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Can't figure something out? Questions, comments, concerns, or other feedback:
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