Package: CHETAH 1.21.0

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]

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CHETAH.pdf |CHETAH.html✨
CHETAH/json (API)
NEWS

# 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-1.21.0(bioc 3.20)CHETAH-1.20.0(bioc 3.19)

bioconductor-package

9 exports 0.71 score 104 dependencies 6 mentions

Last updated 2 months agofrom:4634009583

Exports:CHETAHclassifier CHETAHshiny Classify ClassifyReference CorrelateReference PlotCHETAH PlotTree PlotTSNE RenameBelowNode

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

Introduction to the CHETAH package

Jurrian de Kanter

Rendered fromCHETAH_introduction.Rmdusingknitr::rmarkdownon Jun 30 2024.

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 1.21.0

CHETAH: Fast and accurate scRNA-seq cell type identification

Introduction to the CHETAH package

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)