CHETAH

DOI: 10.18129/B9.bioc.CHETAH    

Fast and accurate scRNA-seq cell type identification

Bioconductor version: Release (3.14)

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

BiocManager::install("CHETAH")

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

Documentation

PDF		Reference Manual

Details

biocViews	Classification, Clustering, RNASeq, SingleCell, Software
Version	1.10.0
In Bioconductor since	BioC 3.9 (R-3.6) (3 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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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