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Cidane
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Cidane

A tool to assemble ab initio and quantify transcripts in RNA-seq data. The Cidane algorithm also annotates known splice sites, transcription starts and ends.



Cidane

A tool to assemble ab initio and quantify transcripts in RNA-seq data. The Cidane algorithm also annotates known splice sites, transcription starts and ends.

Topic

RNA splicing; RNA-seq; Gene transcripts

Details

  • Operation: RNA-Seq quantification; De-novo assembly; Splice transcript prediction; Gene expression profiling
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux
  • License: GNU General Public License v3
    • Cost: Free
  • Version name: 0.0.1
    • Maturity: Stable
  • Credit: The National Institutes of Health (NIH)
  • Contact: David Weese david.weese _at_ fu-berlin.de | Knut Reinert knut.reinert _at_ fu-berlin.de | Gunnar W. Klau gunnar.klau _at_ cwi.nl
  • Collection: -

Publications

Canzar S, Andreotti S, Weese D, Reinert K, Klau GW "CIDANE: comprehensive isoform discovery and abundance estimation." Genome Biol. 2016 Jan 30;17:16. https://doi.org/10.1186/s13059-015-0865-0
PMID: 26831908
PMCID: PMC4734886


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