# Fast and accurate scRNA-seq cell type identification

## Documentation for package ‘CHETAH’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

CHETAHclassifier | Identification of cell types aided by hierarchical clustering
CHETAHshiny | Launch a web page to interactively go trough the classification
Classify | (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.
ClassifyReference | Use a reference dataset to classify itself. A good reference should have almost no mixture between reference cells.
CorrelateReference | Correlate all reference profiles to each other using differentially expressed genes.
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.
PlotCHETAH | Plot the CHETAH classification on 2D visulization like t-SNE + the corresponding classification tree, colored with the same colors
PlotTree | Plots the chetah classification tree with nodes numbered
PlotTSNE | Plots a variable on a t-SNE
RenameBelowNode | In the CHETAH classification, replace the name of a Node and all the names of the final and intermediate types under that Node.