CHETAH
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 (3.20)
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("CHETAH")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")
Introduction to the CHETAH package | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Classification, Clustering, GeneExpression, ImmunoOncology, RNASeq, SingleCell, Software |
Version | 1.21.0 |
In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
License | file LICENSE |
Depends | R (>= 4.2), ggplot2, SingleCellExperiment |
Imports | 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 | adverSCarial |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | CHETAH_1.21.0.tar.gz |
Windows Binary (x86_64) | CHETAH_1.21.0.zip |
macOS Binary (x86_64) | CHETAH_1.21.0.tgz |
macOS Binary (arm64) | CHETAH_1.21.0.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 |