|HOMER (Hypergeometric Optimization of Motif EnRichment) is
a suite of tools for Motif Discovery and next-gen sequencing
analysis. It is a collection of command line programs
for unix-style operating systems written in Perl and C++.
HOMER was primarily written as a de novo motif discovery algorithm and is
well suited for finding 8-20 bp motifs in large scale
genomics data. HOMER contains many useful tools for
analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and
numerous other types of functional genomics sequencing data
New version v4.6. Better super enhancer
code, plus lots of other minor upgrades.
(1-27-2014) New version v4.5 with updated
genome packages too - Last version did not
correctly assign priority assignments in
annotations (i.e. TSS > exons >
introns > intergenic was not honored in
last version - fixed now). Problems
with some of the update scripts too.
Website updates are ongoing.
(1-23-2014) Updated All Organism Packages to v1.1
- latest packages lacked the org2gene.tsv
file (i.e. human2gene.tsv). Users that
updated from the older version of HOMER probably
didn't notice since the old files would have still
been there - new users probably got an error.
(1-15-2014) Welcome to homer.salk.edu - new host for
(1-15-2014) Lots of new documentation. More new
documentation will probably be added to the site over
the next week or so, and new PDF's will be created
once that gets in good shape.
(1-14-2014) New version v4.4. New version with changes
to configuration to help separate the code and data,
update scripts to keep annotation/accessions
up-to-date and incorporate custom
genomes/organisms. As always, lots of new
features and bug fixes. It's very likely a new
version will be posted soon to smooth out any
details. Major changes to note:
- Major Updates to annotations and custom
configuration - easier to add your own genome or
- bedGraphs and coverage histrograms are now
normalized for fragment length (this is a GOOD
upgrade, be careful comparing to old results)
Page - Get the latest version of HOMER
Organisms: Human (hg17, hg18, hg19),
Mouse (mm8, mm9, mm10), Rat (rn4, rn5), Frog
(xenTro2, xenTro3), Zebrafish (danRer7),
Drosophila (dm3), C elegans (ce6, ce10), S.
cerevisiae (sacCer2, sacCer3), pombe (ASM294v1),
Arabidopsis (tair10), Rice (msu6), and also works
with custom genomes in FASTA format and gene
annotations in GTF format.
Hi-C Analysis Tutorial [PDF-old]
Description of routines for analysis of Hi-C
data to study genome conformation and structure.
Primary Data Download
UCSC Visualization files (Updated for errors in UCSC
HOMER Known Motifs - Genome-wide predictions and UCSC
Data included in HOMER that may be useful for other
HOMER was developed
primarily by Chris Benner, with significant contributions
and suggestions by Sven Heinz, Kasey Hutt, Yin Lin, Gene
Hsiao, Fernando Alcalde, Josh Stender, Amy Sullivan,
Nathan Spann, Ivan Garcia-Bassets, Michael Lam, Michael
Rehli, and many others. Initial supervision for the
project was provided by Professors Christopher K. Glass
and Shankar Subramaniam.
Development of HOMER is carried out in the Integrative Genomics and
at the Salk Institute
HOMER was initially developed in the Glass
Lab at UCSD
For now, if you use HOMER in your research, please cite
the following paper:
Simple Combinations of
Lineage-Determining Transcription Factors Prime
cis-Regulatory Elements Required for Macrophage and B
Cell Identities. Mol Cell
2010 May 28;38(4):576-589. PMID: 20513432