HOMER

HOMER v4.9.1 type access

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. 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.

For more information, check here.

HOMER utilities
  • analyzeHiC

  • analyzeRepeats

  • analyzeRNA

  • annotateInteractions

  • annotatePeaks

  • annotateTranscripts

  • bed2pos

  • checkPeakFile

  • compareMotifs

  • findGO

  • findHiCCompartments

  • findHiCInteractionsByChr

  • findMotifs

  • findMotifsGenome

  • findPeaks

  • getDifferentialPeaks

  • getHiCcorrDiff

  • homerTools

    • barcodes

    • cluster

    • decontaminate

    • extract

    • freq

    • trim

    • truseq

  • loadPromoters

  • makeTagDirectory

  • makeUCSCfile

  • mergePeaks

  • motif2Logo

  • pos2bed

  • removeOutOfBoundsReads

  • revoppMotif

  • runHiCpca

  • seq2profile

  • SIMA

  • tagDir2bed