Visualization of Clonal Expansion for Single Cell Immune Profiles

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Documentation for package ‘APackOfTheClones’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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