Introduction

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/OEFinderrstewart@morgridge.org or lengning1@gmail.comSupplementary data are available at Bioinformatics online.

Publications

  1. OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.
    Cite this
    Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R, 2016-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Ning Leng
    Developer

  2. Jeea Choi
    Developer

  3. Li-Fang Chu
    Developer

  4. James A Thomson
    Developer

  5. Christina Kendziorski
    Developer

    Department of Biostatistics and Medical Informatics, University of Wisconsin, United States of America

  6. Ron Stewart
    Investigator

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Summary
AccessionBT001535
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByRon Stewart