CHETAH

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see CHETAH.

Fast and accurate scRNA-seq cell type identification


Bioconductor version: 3.12

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 "4.0") 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, RNASeq, SingleCell, Software
Version 1.6.0
In Bioconductor since BioC 3.9 (R-3.6) (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
System Requirements
URL https://github.com/jdekanter/CHETAH
Bug Reports https://github.com/jdekanter/CHETAH
See More
Suggests knitr, rmarkdown, Matrix, testthat, vdiffr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package CHETAH_1.6.0.tar.gz
Windows Binary CHETAH_1.6.0.zip
macOS 10.13 (High Sierra) CHETAH_1.6.0.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
Old Source Packages for BioC 3.12 Source Archive