all_sample_all_chain_all_metrics_wide_format_dataframe |
a dataframe of wide format |
all_sample_all_chain_all_metrics_wide_format_dataframe_list |
a dataframe list to combine rowwise. |
all_sample_all_chain_individual_metrics_dataframe_list |
a list of dataframes |
all_sample_IGH_chain_all_metrics_wide_format_dataframe |
a dataframe of wide format |
all_sample_IGH_chain_all_metrics_wide_format_dataframe_list |
a dataframe list to combine rowwise. |
all_sample_IGH_chain_individual_metrics_dataframe_list |
a list of dataframes |
annotate_chain_name_and_isotype_name |
Annotate chain name and isotype name |
calculate_IGH_isotype_proportion |
calculate_IGH_isotype_proportion |
calculate_repertoire_metrics |
calculate_repertoire_metrics |
calibrate_proportion_by_clones |
calibrate_proportion_by_clones |
chain_separated_dataframe |
a dataframe separated by chain name |
combine_all_sample_repertoire_metrics |
combine_all_sample_repertoire_metrics |
compute_repertoire_metrics_by_chain_name |
compute_repertoire_metrics_by_chain_name |
convergent_clonotype_merged_dataframe |
a dataframe where convergent clonotypes are merged |
format_clonotype_to_immunarch_style |
Convert clonotype dataframe to immunarch format |
get_item_name_x_sample_name_for_each_metric |
get_item_name_x_sample_name_for_each_metric |
immunarch_style_dataframe |
An converted dataframe to immunarch format |
merge_convergent_clonotype |
Merge convergent clonotype |
nonproductive_CDR3aa_removed_dataframe |
a dataframe with nonproductive CDR3aa removed |
parse_mixcr |
Parse mixcr format |
parse_trust4 |
Parse trust4 format |
raw_input_clonotype_dataframe |
Raw clonotype output from trust4 |
remove_nonproductive_CDR3aa |
Clean the clonotype dataframe |
summarize_convergence_function |
summarize_convergence_function |
summarize_repertoire_metrics |
summarize_repertoire_metrics |
the global variables |
Make variable names global to avoid CHECK notes |
the_divergent_clonotype_dataframe_list |
a list of dataframe where convergent clonotypes are merged |