For better experience, turn on JavaScript!


cellity

cellity

cellity is a tool to detect and filter cells in single-cell RNA-seq data. The cellity algorithm works based on over 20 curated sets of biological and experimental characteristics. A Python version is also available, see links.

Topic

Cell biology; RNA-Seq; Data quality management

Details

  • Operation: Sequencing quality control
  • Software interface: Command-line user interface; Library
  • Language: R;Python
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v>=2
  • Cost: Free
  • Version name: -
  • Maturity: Mature
  • Credit: BBSRC CASE Studentship, the Lister Institute, NHRMC Early Career Fellow, The Lundbeck Foundation, The European Molecular Biology Laboratory (EMBL), the Wellcome Sanger Institute (WTSI).
  • Contact: Sarah A. Teichmann ti243 _at_ cam.ac.uk
  • Collection: BioConductor

Publications

Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA "Classification of low quality cells from single-cell RNA-seq data." Genome Biol. 2016 Feb 17;17:29. https://doi.org/10.1186/s13059-016-0888-1
PMID: 26887813
PMCID: PMC4758103


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


Download and documentation








If you find errors, please report here.