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. |