CHETAH
This is the released version of CHETAH; for the devel version, see CHETAH.
Fast and accurate scRNA-seq cell type identification
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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, GeneExpression, ImmunoOncology, RNASeq, SingleCell, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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_1.28.0.tar.gz |
| Windows Binary (x86_64) | CHETAH_1.28.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CHETAH_1.28.0.tgz |
| macOS Binary (sonoma-arm64) | CHETAH_1.28.0.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 |