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Hypergeometric Optimization of Motif EnRichment HOMER

A suite of tools for Motif Discovery and next-gen sequencing analysis. 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.

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5 user reviews

5 user reviews

Mano's avatar image Mano's country flag


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

Anand Mt's avatar image

Anand Mt

This is by far best tool for ChIP seq. Thank you so much authors.

Ka-Chun Wong's avatar image

Ka-Chun Wong

Homer is one of the best available motif discovery software suite on the internet, especially for next-generation sequencing. I highly recommend it.

Fabien Pichon's avatar image Fabien Pichon's country flag

Fabien Pichon

An amazing tool suite !!! Indispensable !
Orginally created for motif discovery from .fasta file or peak file, you can also use it to compare peaks between different experiments. Better than bedtools because it gives you all details, ideal to create Venn diagrams. You can also use it to extract DNA sequences from regions. This is the swiss knife for genomics !!!!

Claudia Armenise Quartz Bio's avatar image

Claudia Armenise Quartz Bio

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

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HOMER classification

HOMER specifications

Software type:
Restrictions to use:
Computer skills:
Command line interface
Operating system:


  • findMotifs
  • findMotifsGenome
  • scanMotifGenomeWide
  • compareMotifs

HOMER distribution


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Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA

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