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CONICS

CONICS

CONICS (COpy-Number analysis In single-Cell RNA-Sequencing) is a tool to analyze copy-number variation (CNV) in single-cell RNA-seq data. CONICS quantifies CNV, maps gene expressions to tumor clones, and phylogenies.

Topic

RNA-seq; DNA structural variation; Genetic variation

Details

  • Operation: DNA mapping; Copy number estimation
  • Software interface: Command-line user interface
  • Language: R;Perl;Python
  • Operating system: Linux; Mac OS X
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: Cancer League Research Grant, a NCI Helen Diller Family Comprehensive Cancer Center, UCSF Brain Tumor SPORE Career Development Award, the Dabbiere Family.
  • Contact: Aaron Diaz aaron.diaz _at_ ucsf.edu
  • Collection: -

Publications

Muller S, Cho A, Liu SJ, Lim DA, Diaz A "CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones." Bioinformatics. 2018 Sep 15;34(18):3217-3219. https://doi.org/10.1093/bioinformatics/bty316
PMID: 29897414


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