HOMER pipeline

HOMER specifications

Information


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

Subtools


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

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Maintainers


  • person_outline Christopher Glass <>
  • person_outline Christopher Benner <>

Publication for Hypergeometric Optimization of Motif EnRichment

HOMER IN pipelines

 (24)
2018
PMCID: 5785540
PMID: 29371665
DOI: 10.1038/s41467-017-02740-5

[…] standard illumina protocol (hiseq2000, single read, 50 bp v3), and mapped to the mouse mm10 reference genome by bowtie45. data were further analyzed using the peak finding algorithm macs 1.4.246. homer software was used to annotate peaks47, and all peaks with false discovery rate <1% were included. the uniquely mapping locations were used to generate the genome-wide intensity profiles, […]

2018
PMCID: 5873942
PMID: 29590119
DOI: 10.1371/journal.pone.0193126

[…] for nf90/nf110 chip-seq data was performed in r with the chipseeker package and deeptools [74, 75]. motif enrichment analysis and gene annotation of nf90/nf110 chip-seq peaks were computed using hypergeometric optimization of motif enrichment (homer) [76]. nf90/nf110 occupancy frequency in each chromatin state was computed in r with the diffbind package [77]., relative enrichment […]

2017
PMCID: 5253667
PMID: 28112213
DOI: 10.1038/srep41063

[…] consortium (http://genome.ucsc.edu/encode/encodetools.html). moreover, we obtained average pbc scores. irreproducible discovery rate procedure (idr v 2.0.2) following encode guidelines32, and using homer (v4.7.2)33 as peak caller, was performed to measure sample reproducibility and to identify consistent peaks. homer parameters were set according to the authors’ indication for idr calculation […]

2017
PMCID: 5253667
PMID: 28112213
DOI: 10.1038/srep41063

[…] discovery rate procedure (idr v 2.0.2) following encode guidelines32, and using homer (v4.7.2)33 as peak caller, was performed to measure sample reproducibility and to identify consistent peaks. homer parameters were set according to the authors’ indication for idr calculation (-p. 1 –lp. 1 –poisson. 1), -l was set to three. the “findpeaks score” column was selected as ranking column for idr […]

2017
PMCID: 5253667
PMID: 28112213
DOI: 10.1038/srep41063

[…] sample reproducibility and to identify consistent peaks. homer parameters were set according to the authors’ indication for idr calculation (-p. 1 –lp. 1 –poisson. 1), -l was set to three. the “findpeaks score” column was selected as ranking column for idr calculations, as suggested by homer authors. the pool of two independent input preparations was used as background for the analysis, […]

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

 (4)
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Gyan Prakash Mishra

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Desktop
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.

Mano

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