msCentipede

msCentipede is a tool to identify transcription binding sites in tissue-specific DNase I cleavage patterns and genomic sequence content. The msCentipede algorithm uses multi-scale models for inhomogeneous Poisson processes, to access variation in DNase I cleavage patterns.

Topic

Transcription factors and regulatory sites

Detail

  • Operation: Transcription factor binding site prediction

  • Software interface: Command-line user interface

  • Language: Python

  • License: The MIT licence

  • Cost: Free

  • Version name: 1.0

  • Credit: NIH, the Howard Hughes Medical Institute

  • Input: -

  • Output: -

  • Contact: mstephens@uchicago.edu

  • Collection: -

  • Maturity: -

Publications

  • msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.
  • Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. PLoS One. 2015 Sep 25;10(9):e0138030.
  • https://doi.org/10.1371/journal.pone.0138030
  • PMID: 26406244
  • PMC: PMC4583425

Download and documentation

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