README.md

In CHETAH: Fast and accurate scRNA-seq cell type identification

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: ```{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 ```

CHETAH documentation built on Nov. 8, 2020, 8:02 p.m.