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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Versioning
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Maintainers
- person_outline Christopher Glass <>
- person_outline Christopher Benner <>
HOMER article
HOMER citations
(13)Id Proteins Suppress E2A-Driven Invariant Natural Killer T Cell Development prior to TCR Selection
[…] 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 […]
[…] 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 […]
Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation
[…] 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, […]
[…] 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 […]
A chemical screen in zebrafish embryonic cells establishes that Akt activation is required for neural crest development
[…] 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 reviews
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