Repertoire Analysis of the Detected Clonotype
Documentation for package ‘rTCRBCRr’ version 0.1.0
DESCRIPTION file
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User guides, package vignettes and other documentation.
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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_divergent_clonotype_dataframe_list
a list of dataframe where convergent clonotypes are merged