clustifyr: an R package for automated single-cell RNA sequencing cluster classification [version 1; peer review: 2 approved with reservations]

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...

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Bibliographic Details
Published inF1000 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
LanguageEnglish
Published England 2020
Subjects
Gene Expression Profiling
Humans
RNA, Small Cytoplasmic
Sequence Analysis, RNA - methods
Single-Cell Analysis
Software
cell type classification
gene expression profile
Single-cell RNA sequencing
R package
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Summary: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 Abbreviations: PBMC: peripheral blood mononuclear cell; scRNA-seq: single-cell RNA sequencing; SCE: SingleCellExperiment.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.22969.1