Package: CHETAH 1.29.0

Jurrian de Kanter

CHETAH: Fast and accurate scRNA-seq cell type identification

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.

Authors:Jurrian de Kanter [aut, cre], Philip Lijnzaad [aut]

CHETAH_1.29.0.tar.gz
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CHETAH_1.29.0.tgz(r-4.6-any)CHETAH_1.29.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CHETAH/json (API)

# Install 'CHETAH' in R:

install.packages('CHETAH', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jdekanter/chetah/issues

Datasets:

headneck_ref - A SingleCellExperiment with celltypes in the "celltypes" colData. A subset of the Head-Neck data from Puram et al. (2017) Cancer Cell.
input_mel - A SingleCellExperiment on which CHEATHclassifier is run using the 'headneck_ref' It holds subset of the Melanoma data, from Tirosh et al. (2016), Science.

On BioConductor:CHETAH-1.29.0(bioc 3.24)CHETAH-1.28.0(bioc 3.23)

classification rnaseq singlecell clustering geneexpression immunooncology

7.49 score 44 stars 78 scripts 404 downloads 6 mentions 9 exports 96 dependencies

Last updated from:21dc479e20. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	180
linux-devel-x86_64	OK	367
source / vignettes	OK	266
linux-release-x86_64	OK	344
macos-release-arm64	OK	279
macos-oldrel-arm64	OK	225
windows-devel	OK	261
windows-release	OK	256
windows-oldrel	OK	253
wasm-release	OK	136

Exports:CHETAHclassifier CHETAHshiny Classify ClassifyReference CorrelateReference PlotCHETAH PlotTree PlotTSNE RenameBelowNode

Dependencies:abind askpass base64enc Biobase BiocGenerics bioDist bslib cachem cli commonmark corrplot cowplot cpp11 crosstalk curl data.table DelayedArray dendextend digest dplyr evaluate farver fastmap fontawesome fs generics GenomicRanges ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pheatmap pillar pkgconfig plotly plyr promises purrr R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo shiny SingleCellExperiment sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex utf8 vctrs viridis viridisLite withr xfun xtable XVector yaml

Introduction to the CHETAH package

Rendered fromCHETAH_introduction.Rmdusingknitr::rmarkdown

Last update: 2022-07-08
Started: 2019-02-17

Help page	Topics
Identification of cell types aided by hierarchical clustering	CHETAHclassifier
Launch a web page to interactively go trough the classification	CHETAHshiny
(Re)classify after running 'CHETAHclassifier' using a confidence threshold NOTE: In case of bulk reference profiles: only the correlations will be used, as the data does not allow for profile or confidence scores to be calculated.	Classify
Use a reference dataset to classify itself. A good reference should have almost no mixture between reference cells.	ClassifyReference
Correlate all reference profiles to each other using differentially expressed genes.	CorrelateReference
A SingleCellExperiment with celltypes in the "celltypes" colData. A subset of the Head-Neck data from Puram et al. (2017) Cancer Cell.	headneck_ref
A SingleCellExperiment on which CHEATHclassifier is run using the 'headneck_ref' It holds subset of the Melanoma data, from Tirosh et al. (2016), Science.	input_mel
Plot the CHETAH classification on 2D visulization like t-SNE + the corresponding classification tree, colored with the same colors	PlotCHETAH
Plots the chetah classification tree with nodes numbered	PlotTree
Plots a variable on a t-SNE	PlotTSNE
In the CHETAH classification, replace the name of a Node and all the names of the final and intermediate types under that Node.	RenameBelowNode

Package: CHETAH 1.29.0

CHETAH: Fast and accurate scRNA-seq cell type identification

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