clustifyr: an R package for automated single-cell RNA sequencing cluster classification [version 2; peer review: 2 approved]

• Published in: F1000 research Vol. 9; p. 223
• Main Authors: Fu, Rui, Gillen, Austin E, Sheridan, Ryan M, Tian, Chengzhe, Daya, Michelle, Hao, Yue, Hesselberth, Jay R, Riemondy, Kent A
• Format: Journal Article
• Language: English
• Published: London Faculty of 1000 Ltd 2020; F1000 Research Limited; F1000 Research Ltd
• Subjects: Automation; Data analysis; Datasets; DNA microarrays; Gene expression; Metadata; Ribonucleic acid; RNA; Software Tool; cell type classification; gene expression profile; Single-cell RNA sequencing; R package
• ISSN: 2046-1402; 2046-1402
• DOI: 10.12688/f1000research.22969.2

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 https://github.com/rnabioco/clustifyr