CHETAH
Fast and accurate scRNA-seq cell type identification
Bioconductor version: Release (3.17)
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 "4.3") 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, GeneExpression, ImmunoOncology, RNASeq, SingleCell, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (4.5 years) |
| License | file LICENSE |
| Depends | R (>= 4.2), ggplot2, SingleCellExperiment |
| Imports | shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment |
| Linking To | |
| Suggests | knitr, rmarkdown, Matrix, testthat, vdiffr |
| System Requirements | |
| Enhances | |
| URL | https://github.com/jdekanter/CHETAH |
| Bug Reports | https://github.com/jdekanter/CHETAH |
See More
| 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_1.16.0.tar.gz |
| Windows Binary | CHETAH_1.16.0.zip (64-bit only) |
| macOS Binary (x86_64) | CHETAH_1.16.0.tgz |
| macOS Binary (arm64) | CHETAH_1.16.0.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 |