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 |