CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

CHETAH is an R package for cell type identification of single-cell RNA-sequencing (scRNA-seq) data. Cell types are assigned by correlating the input data to a reference in a hierarchical manner. CHETAH is built to work with scRNA-seq references, but will also work (with limited capabilities) with RNA-seq or micro-array reference datasets.

The article describing CHETAH can be found at: Nucleic Acids Research.

CHETAH is now part of Bioconductor.

CHETAH can be installed by running:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CHETAH")

To get to know the basics of the CHETAH pacakge, please look at the vignette;

vignette("CHETAH_introduction")

At a glance: to run chetah on an input count matrix input_counts with t-SNE coordinates in input_tsne, and a reference count matrix ref_counts with celltypes vector ref_ct, run:

## Make SingleCellExperiments
reference <- SingleCellExperiment(assays = list(counts = ref_counts),
                                     colData = DataFrame(celltypes = ref_ct))

input <- SingleCellExperiment(assays = list(counts = input_counts),
                              reducedDims = SimpleList(TSNE = input_tsne))

## Run CHETAH
input <- CHETAHclassifier(input = input, ref_cells = reference)

## Plot the classification
PlotCHETAH(input)

## Extract celltypes:
celltypes <- input$celltype_CHETAH