Awesome
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