clustifyr: an R package for automated single-cell RNA sequencing cluster classification

F1000Res. 2020 Apr 1;9:223. doi: 10.12688/f1000research.22969.2. eCollection 2020.


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

Keywords: R package; Single-cell RNA sequencing; cell type classification; gene expression profile.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling
  • Humans
  • RNA, Small Cytoplasmic*
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis*
  • Software*


  • RNA, Small Cytoplasmic

Associated data

  • figshare/10.6084/m9.figshare.5435866.v8