RT Journal Article
SR Electronic
T1 OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 025437
DO 10.1101/025437
A1 Ning Leng
A1 Jeea Choi
A1 Li-Fang Chu
A1 James A. Thomson
A1 Christina Kendziorski
A1 Ron Stewart
YR 2015
UL http://biorxiv.org/content/early/2015/08/25/025437.abstract
AB A recent paper identified an artifact in multiple single-cell RNA-seq (scRNA-seq) data sets 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 that allows users to check for potential artifacts in scRNA-seq data generated by the Fluidigm C1 platform.Availability and Implementation OEFinder is freely available at https://github.com/lengning/OEFinderContact rstewart{at}morgridge.org