ChromNet

ChromNet is a web-based tool to visualize and identify interactions among ChIP-seq datasets. ChromNet represents interactions using hierarchical clustering, direct group interactions by edges, and color intensity. Users can also directly search all ENCODE ChIP-seq tracks by ID.

Topic

ChIP-seq;Data visualisation;Molecular interactions, pathways and networks

Detail

  • Operation: Peak calling;Expression data visualisation

  • Software interface: Web user interface

  • Language: Python

  • License: Web application

  • Cost: Free

  • Version name: -

  • Credit: National Science Foundation (NSF) Graduate Research Fellowship, NSF, Natural Sciences and Engineering Research Council of Canada, Canada Research Chair in Molecular Oncology, Canadian Institute for Health, Canadian Breast Cancer Foundation Ontario Region Doctoral Fellowship.

  • Input: JSON, ID

  • Output: -

  • Contact: Su-In Lee suinlee@uw.edu

  • Collection: -

  • Maturity: -

Publications

  • ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.
  • Lundberg SM, Tu WB, Raught B, Penn LZ, Hoffman MM, Lee SI. ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data. Genome Biol. 2016 Apr 30;17:82. doi: 10.1186/s13059-016-0925-0. PMID: 27139377; PMCID: PMC4852466.
  • https://doi.org/10.1186/s13059-016-0925-0
  • PMID: 27139377
  • PMC: PMC4852466

Download and documentation

< Back to DB search