title: OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.
abstract: A recent article identified an artifact in multiple single-cell RNA-seq (scRNA-seq) datasets generated by the Fluidigm C1 platform. Specifically, Leng et al. showed significantly increased gene expression in cells captured from sites with small or large plate output IDs. We refer to this artifact as an ordering effect (OE). Including OE genes in downstream analyses could lead to biased results. To address this problem, we developed a statistical method and software called OEFinder to identify a sorted list of OE genes. OEFinder is available as an R package along with user-friendly graphical interface implementations which allows users to check for potential artifacts in scRNA-seq data generated by the Fluidigm C1 platform.
  
  
  
  OEFinder is freely available at https://github.com/lengning/OEFinder
  
  
  
  rstewart@morgridge.org or lengning1@gmail.com
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Morgridge Institute for Research.
authors.forename: Ning
authors.initials: N
authors.lastname: Leng
authors.affiliation: Department of Statistics, University of Wisconsin and.
authors.forename: Jeea
authors.initials: J
authors.lastname: Choi
authors.affiliation: Morgridge Institute for Research.
authors.forename: Li-Fang
authors.initials: LF
authors.lastname: Chu
authors.affiliation: Morgridge Institute for Research.
authors.forename: James A
authors.initials: JA
authors.lastname: Thomson
authors.affiliation: Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA.
authors.forename: Christina
authors.initials: C
authors.lastname: Kendziorski
authors.affiliation: Morgridge Institute for Research.
authors.forename: Ron
authors.initials: R
authors.lastname: Stewart
mesh_terms: D000818:Animals; D012313:RNA; D017423:Sequence Analysis, RNA; D059010:Single-Cell Analysis; D012984:Software
chemical_list: D012313:RNA