Visualization of Clonal Expansion for Single Cell Immune Profiles
Adjust the parameters of the APackOfTheClones reduction in a seurat ob...
APackOfTheClones: Visualization of Clonal Expansion for Single Cell Im...
Various variations of visualizations of clonal expansion post-RunAPOTC
DEFUNCT: Visualize T cell clonal expansion with a ball-packing plot.
Check for the existence of an APackOfTheClones run with its run id
DEFUNCT: count the number of clonotype sizes per cell cluster in a seu...
count the number of clonotype sizes in a seurat object combined with a...
Delete the results of an APackOfTheClones run
Get all run ids of previous RunAPOTC runs on a seurat object
Get the object id of the most recent RunAPOTC run on a seurat object
Calculate seurat cluster centroids based on a Dimensional reduction
Compute a list of clonotypes that are shared between seurat clusters
DEFUNCT: Integrate a single TCR library into Seurat object metadata
Merge a list of Clustered Clonotype Frequency Tables
overlay a clone size legend on an APackOfTheClones plot
Remove current APackOfTheClones legend
Rename an APackOfTheClones run
Run the APackOfTheClones method on a combined Seurat object for downst...
Highlight specific clones on an APackOfTheClones ggplot
Directly visualize clonal expansion of a combined seurat object
Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.
Useful links