# 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](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz543/5521789?searchresult=1). > CHETAH is now part of [Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/CHETAH.html). CHETAH can be installed by running: ```{r echo=TRUE, eval=FALSE} 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; ```{r echo=TRUE, eval=FALSE} 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: ```{r glance, echo=TRUE, eval=FALSE} ## 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 ```