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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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If you have landed on this page, you are likely staring at a progress bar that has not moved in the last 20 minutes, or a pop-up notification that keeps flashing the phrase:

If a specific ROM refuse to load or performance is unstable, remember that modern versions of have made massive strides in Namco System 22 emulation. While VivaNonno was the undisputed king for a decade due to its low hardware requirements, MAME now offers highly accurate emulation of these same games with better compatibility for modern USB controllers. The Legacy of Namco System 22

Unlike modern emulators that use complex plugin systems, VivaNonno was built to be lightweight and highly efficient on older Windows operating systems. It uses Direct3D to translate arcade graphics instructions into a language your modern graphics card can process. Supported Games VivaNonno ROM is Downloading...

VivaNonno is not a general-purpose emulator like MAME. It was built with a singular, hyper-focused purpose: to breathe new life into Namco System 22 arcade games on modern PCs. Here is what you need to know while your download finishes. What is VivaNonno?

Go to the Input settings and make sure your device is selected and mapped. Conclusion If you have landed on this page, you

A sci-fi tank combat game utilizing dual-joystick controls. System Requirements

For the authentic look, stick to the original 4:3 aspect ratio. While you can upscale the resolution to match modern monitors, stretching the image to 16:9 will distort the classic polygon models. Controller Mapping It uses Direct3D to translate arcade graphics instructions

Ensure your GPU drivers are up to date. Since the emulator is old, it does not use multi-core processing efficiently; raw single-core clock speed is the primary factor for performance.

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