Gilbert, A. C. | bioRxiv Science

bioRxiv2019

Comparison of marker selection methods for high throughput scRNA-seq data

Here, we evaluate the performance of a variety of marker selection methods on scRNA-seq UMI counts data. We test on an assortment of experimental and synthetic data sets that range in size from several thousand to one million cells. In addition, we propose several performance measures for evaluating the quality of a set of markers when there is no known ground truth. According to these metrics, most existing marker selection methods show similar performance on experimental scRNA-seq data; thus, the speed of the algorithm is the most important consid-eration for large data sets. With this in mind, we introduce RO_SCPCAPANKC_SCPCAPCO_SCPCAPORRC_SCPCAP, a fast marker selection method with strong mathematical underpinnings that takes a step towards sensible multi-class marker selection.

genomics↗

bioRxiv2019

Information Theoretic Feature Selection Methods for Single Cell RNA-Sequencing

Single cell RNA-sequencing (scRNA-seq) technologies have generated an expansive amount of new biological information, revealing new cellular populations and hierarchical relationships. A number of technologies complementary to scRNA-seq rely on the selection of a smaller number of marker genes (or features) to accurately differentiate cell types within a complex mixture of cells. In this paper, we benchmark differential expression methods against information-theoretic feature selection methods to evaluate the ability of these algorithms to identify small and efficient sets of genes that are informative about cell types. Unlike differential methods, that are strictly binary and univariate, information-theoretic methods can be used as any combination of binary or multiclass and univariate or multivariate. We show for some datasets, information theoretic methods can reveal genes that are both distinct from those selected by traditional algorithms and that are as informative, if not more, of the class labels. We also present detailed and principled theoretical analyses of these algorithms. All information theoretic methods in this paper are implemented in our PO_SCPLOWICTUREDC_SCPLOWRO_SCPLOWOCKSC_SCPLOW Python package that is compatible with the widely used scanpy package.

bioinformatics↗