FunChIP

FunChIP is an R/Bioconductor package that allows clustering peaks generated by ChIP-seq based on their functional shape representation. This method captures additional biological information from peak shapes and can be used to classify peaks using a k-mean alignment and clustering algorithm. The package provides a user-friendly pipeline with visualization functions for easy inspection of results. A case study using the transcription factor Myc in 3T9 murine fibroblasts demonstrates that different clusters of peaks with unique shapes are related to distinct genomic locations and transcriptional regulatory activities.

Topic

ChIP-seq

Detail

  • Operation: Peak calling

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: Artistic-2.0

  • Cost: Free

  • Version name: 1.24.0

  • Credit: The “Data-Driven Genomic Computing (GenData 2020)” PRIN project (2013–2015), the “Genomic Computing Project”, a research program involving the European Institute of Oncology, the Istituto Italiano di Tecnologia and the Politecnico di Milano.

  • Input: -

  • Output: -

  • Contact: Alice Parodi alicecarla.parodi@polimi.it

  • Collection: -

  • Maturity: Stable

Publications

  • FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes.
  • Parodi ACL, et al. FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes. FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes. 2017; 33:2570-2572. doi: 10.1093/bioinformatics/btx201
  • https://doi.org/10.1093/bioinformatics/btx201
  • PMID: 28398543
  • PMC: -

Download and documentation

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