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SCnorm

SCnorm

SCnorm is an R tool to normalize single-cell RNA-seq data. The SCnorm algorithm estimates the sequencing coverage for each gene by quantile regression and uses estimated scaling factors for group-wise calculations for expression levels.

Topic

RNA-seq; Sequence analysis; Gene expression

Details

  • Operation: Standardisation and normalisation; RNA-seq read count analysis
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 1.5.7
  • Maturity: Stable
  • Credit: The National Institutes of Health (NIH), the Morgridge Institute for Research.
  • Contact: Rhonda Bacher rbacher _at_ wisc.edu | Rhonda Bacher rbacher _at_ ufl.edu | Christina Kendziorski kendzior _at_ biostat.wisc.edu
  • Collection: BioConductor

Publications

Bacher R, Chu LF, Leng N, Gasch AP, Thomson JA, Stewart RM, Newton M, Kendziorski C "SCnorm: robust normalization of single-cell RNA-seq data." Nat Methods. 2017 Jun;14(6):584-586. https://doi.org/10.1038/nmeth.4263
PMID: 28418000
PMCID: PMC5473255


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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