CHETAH
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CHETAH.
Fast and accurate scRNA-seq cell type identification
Bioconductor version: 3.9
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")
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Installation
To install this package, start R (version "3.6") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Classification, Clustering, RNASeq, SingleCell, Software |
Version | 1.0.5 |
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_1.0.5.tar.gz |
Windows Binary | CHETAH_1.0.5.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | CHETAH_1.0.5.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 3.9 | Source Archive |