Repertoire Analysis of the Detected Clonotype
Clean the clonotype dataframe
rTCRBCRr: Repertoire Analysis of the Detected Clonotype
summarize_convergence_function
summarize_repertoire_metrics
Make variable names global to avoid CHECK notes
Annotate chain name and isotype name
calculate_IGH_isotype_proportion
calculate_repertoire_metrics
calibrate_proportion_by_clones
combine_all_sample_repertoire_metrics
compute_repertoire_metrics_by_chain_name
Convert clonotype dataframe to immunarch format
get_item_name_x_sample_name_for_each_metric
Merge convergent clonotype
Parse mixcr format
Parse trust4 format
The 'TRUST4' or 'MiXCR' is used to identify the clonotypes. The goal of 'rTCRBCRr' is to process the results from these clonotyping tools, and analyze the clonotype repertoire metrics based on chain names and IGH isotypes. The manuscript is still under preparation for publication for now. The references describing the methods in this package will be added later.