Visualization of Clonal Expansion for Single Cell Immune Profiles


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Documentation for package ‘APackOfTheClones’ version 1.0.0

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AdjustAPOTC Adjust the parameters of the APackOfTheClones reduction in a seurat object
APOTCPlot Various variations of visualizations of clonal expansion post-RunAPOTC
combined_pbmc Example Multi-sampled T-cell seurat object with integrated TCR library
containsApotcRun Check for the existence of an APackOfTheClones run with its run id
countCloneSizes count the number of clonotype sizes per cell cluster in a seurat object combined with a VDJ library
count_clone_sizes DEPRECATED: count the number of clonotype sizes per cell cluster in a seurat object integrated with a TCR library
deleteApotcData Delete the results of an APackOfTheClones run
getApotcDataIds Get all run ids of previous RunAPOTC runs on a seurat object
getLastApotcDataId Get the object id of the most recent RunAPOTC run on a seurat object
getReductionCentroids Calculate seurat cluster centroids based on a Dimensional reduction
mini_seurat_obj Artificially generated Seurat object
RunAPOTC Run the APackOfTheClones method on a combined Seurat object for downstream visualization of clonal expansion
vizAPOTC Directly visualize clonal expansion of a combined seurat object