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CHETAH

Fast and accurate scRNA-seq cell type identification


Bioconductor version: Release (3.18)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CHETAH")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("CHETAH")
Introduction to the CHETAH package HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Classification, Clustering, GeneExpression, ImmunoOncology, RNASeq, SingleCell, Software
Version 1.18.0
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
System Requirements
URL https://github.com/jdekanter/CHETAH
Bug Reports https://github.com/jdekanter/CHETAH
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Suggests knitr, rmarkdown, Matrix, testthat, vdiffr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CHETAH_1.18.0.tar.gz
Windows Binary CHETAH_1.18.0.zip
macOS Binary (x86_64) CHETAH_1.18.0.tgz
macOS Binary (arm64) CHETAH_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CHETAH
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CHETAH
Bioc Package Browser https://code.bioconductor.org/browse/CHETAH/
Package Short Url https://bioconductor.org/packages/CHETAH/
Package Downloads Report Download Stats