title: Normalization and noise reduction for single cell RNA-seq experiments.
abstract: A major roadblock towards accurate interpretation of single cell RNA-seq data is large technical noise resulted from small amount of input materials. The existing methods mainly aim to find differentially expressed genes rather than directly de-noise the single cell data. We present here a powerful but simple method to remove technical noise and explicitly compute the true gene expression levels based on spike-in ERCC molecules.
  
  
  METHODS
  The software is implemented by R and the download version is available at http://wanglab.ucsd.edu/star/GRM.
  
  
  BACKGROUND
  wei-wang@ucsd.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Ding
authors.affiliation: Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA.
authors.forename: Lina
authors.initials: L
authors.lastname: Zheng
authors.affiliation: Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA.
authors.forename: Yun
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA.
authors.forename: Nan
authors.initials: N
authors.lastname: Li
authors.affiliation: Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA.
authors.forename: Haiyang
authors.initials: H
authors.lastname: Jia
authors.affiliation: Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA.
authors.forename: Rizi
authors.initials: R
authors.lastname: Ai
authors.affiliation: Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA.
authors.forename: Andre
authors.initials: A
authors.lastname: Wildberg
authors.affiliation: Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093, USA, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Department of Cellular and Molecular Medicine, University of California, La Jolla, CA 92093, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017423:Sequence Analysis, RNA / Q000379:methods*; D059629:Signal-To-Noise Ratio; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software