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Determining small sets of genetic markers that can identify specific cell populations is thus one of the major objectives of computational analysis of mRNA counts data. Many tools have been developed for marker selection on single cell data; most of them, however, are based on complex statistical models and handle the multi-class case in an ad-hoc manner.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>We introduce <jats:sc>RankCorr<\/jats:sc>, a fast method with strong mathematical underpinnings that performs multi-class marker selection in an informed manner. <jats:sc>RankCorr<\/jats:sc> proceeds by ranking the mRNA counts data before linearly separating the ranked data using a small number of genes. The step of ranking is intuitively natural for scRNA-seq data and provides a non-parametric method for analyzing count data. In addition, we present several performance measures for evaluating the quality of a set of markers when there is no known ground truth. Using these metrics, we compare the performance of <jats:sc>RankCorr<\/jats:sc> to a variety of other marker selection methods on an assortment of experimental and synthetic data sets that range in size from several thousand to one million cells.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusions<\/jats:title>\n<jats:p>According to the metrics introduced in this work, <jats:sc>RankCorr<\/jats:sc> is consistently one of most optimal marker selection methods on scRNA-seq data. Most methods show similar overall performance, however; thus, the speed of the algorithm is the most important consideration for large data sets (and comparing the markers selected by several methods can be fruitful). <jats:sc>RankCorr<\/jats:sc> is fast enough to easily handle the largest data sets and, as such, it is a useful tool to add into computational pipelines when dealing with high throughput scRNA-seq data. <jats:sc>RankCorr<\/jats:sc> software is available for download at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/ahsv\/RankCorr\">https:\/\/github.com\/ahsv\/RankCorr<\/jats:ext-link>with extensive documentation.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-020-03641-z","type":"journal-article","created":{"date-parts":[[2020,10,23]],"date-time":"2020-10-23T09:02:36Z","timestamp":1603443756000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":50,"title":["A rank-based marker selection method for high throughput scRNA-seq data"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5930-8841","authenticated-orcid":false,"given":"Alexander H. 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