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.
