PT  - JOURNAL ARTICLE
AU  - Ning Leng
AU  - Jeea Choi
AU  - Li-Fang Chu
AU  - James A. Thomson
AU  - Christina Kendziorski
AU  - Ron Stewart
TI  - OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data
AID  - 10.1101/025437
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 025437
4099  - http://biorxiv.org/content/early/2015/08/25/025437.short
4100  - http://biorxiv.org/content/early/2015/08/25/025437.full
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