Journal
GENOME BIOLOGY
Volume 21, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-020-02027-x
Keywords
Gene expression; Single cell RNA-seq; Clustering
Funding
- NIH [R01GM122083, P01NS097206]
- Emory University WHSC 2018 Synergy Award
- NSF [R01GM122083, DBI1054905, P20GM109035]
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Cell clustering is one of the most common routines in single cell RNA-seq data analyses, for which a number of specialized methods are available. The evaluation of these methods ignores an important biological characteristic that the structure for a population of cells is hierarchical, which could result in misleading evaluation results. In this work, we develop two new metrics that take into account the hierarchical structure of cell types. We illustrate the application of the new metrics in constructed examples as well as several real single cell datasets and show that they provide more biologically plausible results.
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