scHiCNorm

scHiCNorm is a tool to eliminate systematic biases in single-cell Hi-C data. The scHiCNorm algorithm uses zero-inflated (Poisson and Negative Binomial) and hurdle (Poisson and Negative Binomial) models to remove biases, cutting sites, GC content, and mappability. The package includes bias features for human (hg19 and hg38) and mouse (mm9 and mm10).

Topic

Sequencing;Sequence analysis;Data quality management;Statistics and probability

Detail

  • Operation: Sequencing quality control

  • Software interface: Command-line user interface

  • Language: Perl, R

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: National Institutest of Health (NIH), University of Miami (UM)

  • Input: -

  • Output: -

  • Contact: zwang@cs.miami.edu

  • Collection: -

  • Maturity: Stable

Publications

  • scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data.
  • Liu T, Wang Z. scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data. Bioinformatics. 2018 Mar 15;34(6):1046-1047. doi: 10.1093/bioinformatics/btx747. PMID: 29186290; PMCID: PMC5860379.
  • https://doi.org/10.1093/bioinformatics/btx747
  • PMID: 29186290
  • PMC: PMC5860379

Download and documentation

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