Fruitstand.7z -

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

Fruitstand.7z -

: A classic example for practicing the use of Arrays, Lists, or HashMaps to store item names and quantities. How to Access the Content To see exactly what is inside your specific version:

: If you don't have it, you'll need the 7-Zip utility or a compatible extractor like WinRAR.

If this file is from a standard programming curriculum or GitHub repository, it likely includes: FruitStand.7z

: Right-click the file and select "Extract to FruitStand/".

: Simple text or JSON files containing the "inventory" of the stand (e.g., apple: $0.50 , banana: $0.30 ). Common Use Cases : A classic example for practicing the use

: Used to demonstrate classes (e.g., a Fruit base class with Apple and Orange subclasses).

: If it is a graphical project (like a 3D rendering demo), it may contain textures, 3D models (like apples, oranges, or a wooden stand), and shader files. : Simple text or JSON files containing the

: Often used in Vulkan or DirectX tutorials as a simple scene to test lighting, shadows, and 3D object loading.

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