CHETAH

DOI: 10.18129/B9.bioc.CHETAH    

This is the development version of CHETAH; to use it, please install the devel version of Bioconductor.

Fast and accurate scRNA-seq cell type identification

Bioconductor version: Development (3.10)

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 "3.6") 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

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 1.1.5
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
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_1.1.5.tar.gz
Windows Binary CHETAH_1.1.5.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) CHETAH_1.1.5.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

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