Homer Software and Data Download (original) (raw)
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 mostly in Perl and C++, although some functionality requires additional tools to be installed as well (e.g. samtools, R, etc.). 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 sets.
News
(07-16-2024) HOMER2 - new version (v5.1). Improvements to some command structure, documentation, data/annotation updates.
(04-25-2024) HOMER2 - new version (v5). Added additional support for positional sequence analysis, including expanded options for background sequence selection and modeling and variant analysis. For more information on these updates, see the HOMER2 page.
(10-24-2019) New version (v4.11) Added routines for csRNA-seq (TSS) analysis. Documentation is here, paper here.
(10-24-2019) Updated genome-wide motif prediction tracks (see below)
(04-01-2019) Check out Metascape for gene enrichment and functional analysis (paper).
Program Download
Download Page - Get the latest version of HOMER (Distributed under GPLv3)
Supported Organisms: Most HOMER tools will work with any FASTA or GTF file, however, additional annotation support is included/available for Human (hg18, hg19, hg38), Mouse (mm8, mm9, mm10), Rat (rn4, rn5, rn6), Frog (xenTro2, xenTro3), Zebrafish (danRer7), Drosophila (dm3), C elegans (ce6, ce10), S. cerevisiae (sacCer2, sacCer3), pombe (ASM294v1), Arabidopsis (tair10), Rice (msu6).
Using HOMER
Introduction to HOMER
_Duff_-sponsored Tutorials
Primary Motif Data
HOMER Known Motifs - Genome-wide predictions and UCSC Track
Data included in HOMER that may be useful for other purposes
Credits
HOMER was developed primarily by Chris Benner, with significant contributions and suggestions by Sven Heinz, Max Chang, Kasey Hutt, Yin Lin, Gene Hsiao, Fernando Alcalde, Josh Stender, Amy Sullivan, Nathan Spann, Ivan Garcia-Bassets, Michael Lam, Michael Rehli, Sascha Duttke, 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 Benner Lab at UCSD, and has been previously been developed in the Integrative Genomics and Bioinformatics Core at the Salk Institute and the Glass Lab at UCSD.
If you use HOMER in your research, generally it is appropriate to cite the following paper:
Heinz S, Benner C, Spann N, Bertolino E et al. 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
For certain specialized analysis, it may be more appropriate to cite one of the following papers:
csRNA-seq/TSS analysis: PMID: 31649059, Hi-C: PMID:30146161, PMID:26417104, PMID:23064439, GRO-seq: PMID:21572438