TY - JOUR T1 - OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data JF - bioRxiv DO - 10.1101/025437 SP - 025437 AU - Ning Leng AU - Jeea Choi AU - Li-Fang Chu AU - James A. Thomson AU - Christina Kendziorski AU - Ron Stewart Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/08/25/025437.abstract N2 - 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 ER -