clustifyr: an R package for automated single-cell RNA sequencing cluster classification
Rui Fu, Austin E. Gillen, Ryan M. Sheridan, Chengzhe Tian, Michelle Daya, Yue Hao, Jay R. Hesselberth, Kent Riemondy
Abstract
<ns4:p> Assignment of cell types from single-cell RNA sequencing (scRNA-seq) data remains a time-consuming and error-prone process. Current packages for identity assignment use limited types of reference data and often have rigid data structure requirements. We developed the clustifyr R package to leverage several external data types, including gene expression profiles to assign likely cell types using data from scRNA-seq, bulk RNA-seq, microarray expression data, or signature gene lists. We benchmark various parameters of a correlation-based approach and implement gene list enrichment methods. clustifyr is a lightweight and effective cell-type assignment tool developed for compatibility with various scRNA-seq analysis workflows. clustifyr is publicly available at <ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="https://github.com/rnabioco/clustifyR">https://github.com/rnabioco/clustifyr</ns4:ext-link> </ns4:p>