HOMER statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HOMER

Tool usage distribution map

This map represents all the scientific publications referring to HOMER per scientific context
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Associated diseases

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Popular tool citations

chevron_left Topology enrichment analysis File format conversion Differential genomic interaction detection Data analysis De novo motif discovery Peak calling Differential motif enrichment analysis Peak annotation Contact matrix normalization Contact matrix generation chevron_right
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HOMER specifications


Unique identifier OMICS_00483
Alternative name Hypergeometric Optimization of Motif EnRichment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


  • annotatePeaks
  • compareMotifs
  • findMotifs
  • findMotifsGenome
  • findPeaks
  • scanMotifGenomeWide




No version available


  • person_outline Christopher Glass
  • person_outline Christopher Benner

Publication for Hypergeometric Optimization of Motif EnRichment

HOMER citations


Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width

Nat Commun
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] To further explore this relationship, we probed additional aspects of genomic architecture. Using a motif analysis algorithm, HOMER, we searched for transcription factor (TF) binding motifs enriched in the subsets of the different geometrical features of H3K4me3 peaks that change or remain consistent during MR. Peak subsets […]


B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

Nat Commun
PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] max = 1000, nstart = 100”. K-means clusters were annotated for enrichment of transcription factor motifs by determining the genome-wide binding motifs of transcription factors defined by the software HOMER, using the function “scanMotifsGenomeWide.pl” and then testing for overrepresentation in each K-means group using Fisher’s exact test. Transcription factor footprinting was calculated by countin […]


PCGF5 is required for neural differentiation of embryonic stem cells

Nat Commun
PMCID: 5954019
PMID: 29765032
DOI: 10.1038/s41467-018-03781-0

[…] d within ±2.5 kb of their TSSs. The density of histone signal was normalized with internal control as described, then visualized by UCSC genome browser. All tag density heatmaps plots were created by homer and in the R package. […]


CD82 hypomethylation is essential for tuberculosis pathogenesis via regulation of RUNX1 Rab5/22

PMCID: 5951854
PMID: 29760437
DOI: 10.1038/s12276-018-0091-4
call_split See protocol

[…] t of condition-specific expression was defined as showing a 1.0 log2-fold difference and P-adj < 0.01 in expression between MTB Rv and MTB Ra. RNA-seq experiments were normalized and visualized using HOMER after preparing custom tracks for the UCSC Genome Browser (http://genome.ucsc.edu/). […]


Comprehensive analysis of coding lncRNA gene co expression network uncovers conserved functional lncRNAs in zebrafish

BMC Genomics
PMCID: 5954278
PMID: 29764394
DOI: 10.1186/s12864-018-4458-7

[…] m transcription factor (TF) families shared by both conserved zebrafish lncRNA and its human counterpart using intersection over union score (Eq. ). TF-binding site prediction was performed using the HOMER tool [].7S=∩TFZTFH∪TFZTFHWhere S is the intersection over union score of upstream TF families shared by both conserved zebrafish lncRNA (TFZ) and its human counterpart (TFH). […]


NOTCH mediated non cell autonomous regulation of chromatin structure during senescence

Nat Commun
PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] To calculate the distance of consensus peaks from TSSs and GC percentage of accessible regions, the Homer (v3.12) command ‘annotatePeaks.pl’ was used with default settings and the output option ‘-CpG’. […]

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HOMER institution(s)
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Section of Molecular Biology, University of California, San Diego, La Jolla, CA, USA; Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA; Department of Discovery Immunology, Genentech, San Francisco, CA, USA; Section of Experimental Haematology, University of Leeds, Leeds, UK
HOMER funding source(s)
Supported by an NIH postdoctoral training grant and by NURSA consortium grant No DK62434 and further supported by NIH grants (HC088093, DK063491, CA52599, P50 GM081892-01A1) and a Foundation Leducq Transatlantic Network Grant.

HOMER reviews

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Gyan Prakash Mishra

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HOMER suite is most widely used for ChIPseq data analysis. Simple command line exposure is sufficient enough to utilize its full potential for diverse array of analysis such as binding region identification (both for TF and histone) , motif analysis, comparison of peaks from multiple experiment and many more.


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One of the best tool for ChIPseq analysis along with downstream analysis till Motif searching and many more.