Package index • VDJigsaw

All functions

annotate_by_clone(): Annotate clone IDs with reference table metadata
assign_clonotype(): Assign clonotypes from raw VDJ contig data
assign_clonotype_from_reference(): Assign clonotypes by mapping to a reference table
clonotype_summary(): Summarize clonotype changes across stringency levels
generate_test_VDJ(): Generate synthetic VDJ contig data for testing
identify_clonotypes(): Identify clonotypes at multiple stringency levels
map_clone_id(): Map clone IDs from VDJigsaw results to wide-format data
map_clonotypes_to_paired_TCR(): Map clonotypes from allele format to paired TCR format
pivot_VDJ(): Pivot VDJ contig data to wide format
plot_clone_composition(): Plot clonotype chain composition
plot_clonotype_flow(): Plot clonotype flow across stringency levels
plot_stringency_summary(): Plot clonotype assignment summary across stringency levels
validate_TCR(): Validate and correct TCR chain data