ChIPseq toolbox

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NGS Analysis of transcriptional regulation

[ Tool-Boxes | Main_Page ]

Standalone tools

  • MACS, MACS2 to find peaks from mapping data.
  • PeakAnalyzer (includes PeakSplitter & PeakAnnotator) from the Bertone Group at EBI.
  • PeakZilla check this!
  • SeqMonk, intuitive NGS analysis GUI from the Babraham Bioinformatics group.
  • SICER from 'A clustering approach for identification of enriched domains from histone modification ChIP-Seq data' by Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao and Weiqun Peng.
  • Homer, standing for Hypergeometric Optimization of Motif EnRichment, is a suite of tools for Motif Discovery and next-gen sequencing analysis

WEB tools

  • ChipSeek integrates several analyses into one WEB ChIP-Seq workflow.
  • The Motif Enrichment Tool ( MET ) takes user-defined gene sets and identifies significantly associated sets of genes that share a regulatory motif ([1]).


Handicon.png Other gDNA NGS tools are listed in the DNAseq toolbox

  1. Charles Blatti, Saurabh Sinha
    Motif enrichment tool.
    Nucleic Acids Res: 2014, 42(Web Server issue);W20-5
    [PubMed:24860165] ##WORLDCAT## [DOI] (I p)

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