Colmek - Funding

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

Colmek - Funding

Provides engineering for systems like the AN/AQS-24A airborne mine-hunting system used by the U.S. Navy. 3. Linguistic Context

| Stakeholder | Pathways to Participation | |-------------|---------------------------| | | Submit an application through the Col‑MiK portal (see Section 4). Attend quarterly “Pitch & Mentor” events hosted in Detroit and New York. | | Academic Researchers | Leverage the Technology Transfer Office (TTO) at Columbia or Michigan to commercialize lab inventions; TTO staff can help package a Colmek Funding proposal. | | Investors / Venture Capitalists | Join the Col‑MiK Investor Network to co‑invest in matched‑funding deals and gain early access to high‑potential pipeline companies. | | Corporate Partners | Offer pilot‑testing facilities, supply‑chain expertise, or joint‑R&D collaborations; corporate partners receive “Strategic Partner” status and can influence program focus areas. | | Policy Makers & NGOs | Provide feedback on program metrics, help shape eligibility criteria, and champion additional public‑funding allocations at the state or federal level. | colmek funding

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)

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