HOMER specifications

Information


Unique identifier OMICS_00483
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


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

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Maintainers


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

HOMER article

HOMER citations

 (13)
2018
PMCID: 5787561

[…] by the ngs: peak annotation tool on nebula (47). bed and wiggle files were generated by macs for visualization using the integrative genomic viewer (48). de novo motif analysis was done using the findmotifs.pl program with homer (49) (v4.7.2, 50, or 200 bp within each peak)., inkt (cd1dtet+ tcrβ+), γδnkt (tcrγδ+ cd3+), and dp (tcrγδ− cd4+ cd8+) cells were sorted from 4- to 5-week-old wt […]

2017
PMCID: 5440673

[…] uniquely mappable reads. the reads of biological replicates and corresponding input samples were merged for peaks calling as previously described50. chip-seq peaks were identified and analysed using homer51 (-f: 2.0, -l: 2.0 and -c: 1.0) with false discovery rate<0.01., the assignment of yap peaks to target genes was obtained by the web tool chipseek52. through this step, it was possible […]

2017
PMCID: 5423031

[…] ebayes. on the basis of the results, each enriched region was grouped either to belong to the 7 days (lost), adult (gained; fdr<0.05) or common (maintained) group (fdr>0.05). the perl script annotatepeaks in homer [54] was used to annotate the 5hmc-enriched regions with various gene features like nearest gene, distance to tts, gene region (5′utr, promoter, exon, intron, intergenic, […]

2017
PMCID: 5253667

[…] 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: 5599238

[…] peak finding algorithm to identify regions of atac-seq peaks, with the following parameter --nomodel --shift −100 --extsize 200. a q-value threshold of enrichment of 0.05 was used for all datasets. homer was used for peak motif analysis (rrid:scr_010881)., this paper was supported by the following grants:, http://dx.doi.org/10.13039/100000002national institutes of health f31ca180313 to christie […]

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

 (5)
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Mano

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Desktop
One of the best tool for ChIPseq analysis along with downstream analysis till Motif searching and many more.
Claudia Armenise Quartz Bio's avatar image No country

Claudia Armenise Quartz Bio

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Desktop
A suite offering a lot of tool, especially for ChIP-sequencing (motif detection, peak overlap, QC...)

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