SimSeq

SimSeq is a software tool that allows for data-based simulation of RNA sequencing (RNA-seq) data, which closely matches the distribution of a source RNA-seq dataset provided by the user. SimSeq enables testing of RNA-seq analysis methods by generating read counts for a given experimental unit with a joint distribution that matches the distribution of the source RNA-seq data

Topic

Genomics

Detail

  • Operation: Modelling and simulation

  • Software interface: Command-line user interface

  • Language: R;Java;C

  • License: Other

  • Cost: Free

  • Version name: -

  • Credit: The National Science Foundation, the National Institute of General Medical Science (NIGMS) of the National Institutes of Health, the joint National Science Foundation/NIGMS Mathematical Biology Program.

  • Input: -

  • Output: -

  • Contact: sgbenidt@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • SimSeq: a nonparametric approach to simulation of RNA-sequence datasets.
  • Benidt S and Nettleton D. SimSeq: a nonparametric approach to simulation of RNA-sequence datasets. SimSeq: a nonparametric approach to simulation of RNA-sequence datasets. 2015; 31:2131-40. doi: 10.1093/bioinformatics/btv124
  • https://doi.org/10.1093/bioinformatics/btv124
  • PMID: 25725090
  • PMC: PMC4481850

Download and documentation

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