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This is the development version of CHETAH; for the stable release version, see CHETAH.

Fast and accurate scRNA-seq cell type identification

Bioconductor version: Development (3.20)

CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is an accurate, selective and fast scRNA-seq classifier. Classification is guided by a reference dataset, preferentially also a scRNA-seq dataset. By hierarchical clustering of the reference data, CHETAH creates a classification tree that enables a step-wise, top-to-bottom classification. Using a novel stopping rule, CHETAH classifies the input cells to the cell types of the references and to "intermediate types": more general classifications that ended in an intermediate node of the tree.

Author: Jurrian de Kanter [aut, cre], Philip Lijnzaad [aut]

Maintainer: Jurrian de Kanter <jurriandekanter at>

Citation (from within R, enter citation("CHETAH")):


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To view documentation for the version of this package installed in your system, start R and enter:

Introduction to the CHETAH package HTML R Script
Reference Manual PDF


biocViews Classification, Clustering, GeneExpression, ImmunoOncology, RNASeq, SingleCell, Software
Version 1.21.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License file LICENSE
Depends R (>= 4.2), ggplot2, SingleCellExperiment
Imports shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment
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Source Package CHETAH_1.21.0.tar.gz
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