DOI: 10.18129/B9.bioc.CHETAH    

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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 (3.15)

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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biocViews Classification, Clustering, RNASeq, SingleCell, Software
Version 1.11.2
In Bioconductor since BioC 3.9 (R-3.6) (2.5 years)
License file LICENSE
Depends R (>= 3.6), ggplot2, SingleCellExperiment
Imports gplots, shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment
Suggests knitr, rmarkdown, Matrix, testthat, vdiffr
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