Title: Classification of low quality cells from single-cell RNA-seq data
Authors: Ilicic, T
Kim, JK
Kolodziejczyk, AA
Bagger, FO
McCarthy, DJ
Marioni, JC
Teichmann, SA
Issue Year: 2016
Publisher BIOMED CENTRAL LTD
Series Genome Biol.:
Abstract Single-cell RNA sequencing (scRNA-seq) has broad applications across biomedical research. One of the key challenges is to ensure that only single, live cells are included in downstream analysis, as the inclusion of compromised cells inevitably affects data interpretation. Here, we present a generic approach for processing scRNA-seq data and detecting low quality cells, using a curated set of over 20 biological and technical features. Our approach improves classification accuracy by over 30 % compared to traditional methods when tested on over 5,000 cells, including CD4+ T cells, bone marrow dendritic cells, and mouse embryonic stem cells.
URI: https://publications.svi.edu.au/publications/1994
ISSN
Other Identifiers 10.1186/s13059-016-0888-1
Publication type Article