CHETAH

DOI: 10.18129/B9.bioc.CHETAH    

Fast and accurate scRNA-seq cell type identification

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Introduction to the CHETAH package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, Clustering, RNASeq, SingleCell, Software
Version	1.8.0
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
LinkingTo
Suggests	knitr, rmarkdown, Matrix, testthat, vdiffr
SystemRequirements
Enhances
URL	https://github.com/jdekanter/CHETAH
BugReports	https://github.com/jdekanter/CHETAH
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CHETAH_1.8.0.tar.gz
Windows Binary	CHETAH_1.8.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	CHETAH_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CHETAH
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CHETAH
Package Short Url	https://bioconductor.org/packages/CHETAH/
Package Downloads Report	Download Stats