HOMER(v5.1, 7-16-2024)
Software for motif discovery and next generation sequencing analysis
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
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
Download file:
Use this file for downloading and updating the full HOMER program and associated data. For sequencing data, there are a bunch of annotation files, etc., for each version of the genome, and this script helps manage those files. If you don't want to deal with configuring HOMER's next-gen sequencing functionality, but want to try it for motif finding, see below.
Instructions: Download configureHomer.pl (right click and select "save link as") and place in a directory dedicated for HOMER (such as homer/).
Run the script by typing "perl configureHomer.pl" - consult the links below for more information. Additional software and configuration will be required the first time you install HOMER (see Installation).
Click for detailed installation instructions
To upgrade, change your directory to where you installed HOMER, and type:
If something appears to be wrong, re-download the "configureHomer.pl" script and use "perl configureHomer.pl -install homer" - this fixes a majority of issues.
Use this file for downloading and updating the full HOMER program and associated data. For sequencing data, there are a bunch of annotation files, etc., for each version of the genome, and this script helps manage those files. If you don't want to deal with configuring HOMER's next-gen sequencing functionality, but want to try it for motif finding, see below.
Instructions: Download configureHomer.pl (right click and select "save link as") and place in a directory dedicated for HOMER (such as homer/).
Run the script by typing "perl configureHomer.pl" - consult the links below for more information. Additional software and configuration will be required the first time you install HOMER (see Installation).
Click for detailed installation instructions
To upgrade, change your directory to where you installed HOMER, and type:
perl configureHomer.pl
-update
- or -
perl configureHomer.pl -install homer (this is good for
forcing the software to reinstall - preferred if you
think there is something wrong) If something appears to be wrong, re-download the "configureHomer.pl" script and use "perl configureHomer.pl -install homer" - this fixes a majority of issues.
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!
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)
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