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ccfindR

ccfindR

ccfindR (Cancer Clone findeR) is a tool for the analysis of cancer cells from single-cell RNA-seq data. ccfindR contains functions for quality control, unsupervised clustering, and visualization. The ccfindR algorithm uses Bayesian non-negative matrix factorization for feature selection and clustering.

Topic

Transcriptomics; Gene structure

Details

  • Operation: Clustering; Phylogenetic tree generation (maximum likelihood and Bayesian methods)
  • Input: RNA count matrix, gene, bar code annotations
  • Output: -
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL>=2
  • Cost: Free
  • Version name: 1.5.1
  • Credit: -
  • Contact: Jinhua Wang jwoo _at_ umn.edu
  • Collection: BioConductor

Publications

Woo J, Winterhoff BJ, Starr TK, Aliferis C, Wang J "De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments." Life Sci Alliance. 2019 Jul 2;2(4). pii: 2/4/e201900443. 10.26508/lsa.201900443. Print 2019 Aug. https://doi.org/10.26508/lsa.201900443
PMID: 31266885
PMCID: PMC6607449


Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590


Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600


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