CHETAH

DOI: 10.18129/B9.bioc.CHETAH    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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 gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.11.2
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
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
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/
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