Package index

TCR-alpha/beta pairing

run_pairing() experimental

Find TCRalpha/beta pairs from individual well read counts

Data loading

load_tirtlseq() experimental

Load data from TIRTLseq experiments

Data wrangling

add_metadata() experimental

Add metadata to a TIRTLseqDataSet object

filter_dataset() experimental

Subset a TIRTLseqDataSet object

reorder_samples() experimental

Re-order samples in a TIRTLseqDataSet object

Data processing and cleaning

TIRTL_process() experimental

Run data processing functions on a TIRTLseqDataSet object

add_single_chain_data() experimental

Add single-chain read counts/fractions to the paired TCR data

clean_pairs() experimental

Remove excess pairs for individual single chains

filter_duplicate_tcrs() experimental

Remove duplicate TCRs from a data frame

filter_mait() experimental

Remove MAIT (Mucosal-Associated Invariant T cells) TCRs

filter_nonfunctional_TCRs() experimental

Remove TCRs with nonfunctional CDR3 amino acid sequences

filter_short_cdr3s() experimental

Remove TCRs with short CDR3 loops

filter_v_alleles() experimental

Remove TCRs with unknown V-segments

identify_non_functional_seqs() experimental

Identify TCRs that contain non-functional CDR3 sequences

identify_paired() experimental

Identify which single chains were paired

prep_for_tcrdist() experimental

Prepare paired TCRs for TCRdist calculation

remove_duplicates() experimental

Removes duplicate paired TCRs

Quality control and data summary

get_all_tcrs() experimental

Returns all of the paired TCRs from all samples in a dataset

get_pair_stats() experimental

Count the number of pairs called by each algorithm

get_paired_by_read_fraction_range() experimental

Calculate the number and fraction of single chains that were paired by frequency

plot_n_reads() experimental

Bar plot of the number of single-chain reads for each sample

plot_num_partners() experimental

Stacked bar plot of the fraction of alpha/beta chains with different numbers of partners

plot_paired() experimental

Stacked bar plot of the number of TCRs paired by each algorithm

plot_paired_by_read_fraction_range() experimental

Bar plot of the fraction of paired single chains by frequency

plot_paired_vs_rank() experimental

A step plot of the cumulative number of paired/unpaired alpha/beta chains among the most frequent chains

plot_pairs_with_eachother() experimental

A connected point plot of read fraction vs. rank for the most frequent alpha/beta chains

plot_ranks() rank_plot() experimental

Line plot of clonotype rank vs. read fraction for each sample

plot_read_fraction_vs_pair_status() experimental

A point plot of read fraction vs. rank for the most frequent alpha/beta chains

plot_sample_overlap() sample_overlap() experimental

Plot the overlap/agreement between samples (in terms of most frequent clones)

summarize_data() experimental

Create a summary table with number of reads and unique alpha/beta chains

TCR similarity and clustering

TCRdist() experimental

GPU implementation of TCRdist, a distance/similarity metric for pairs of TCRs

TCRdist_cpp() experimental

Parallelized C++ implementation of TCRdist (no GPU required)

cluster_tcrs() experimental

Cluster TCRs (using the Leiden algorithm) based on their pairwise TCRdist values

plot_clusters() experimental

Plot clusters of similar TCRs

Longitudinal analysis

plot_clone_size_across_samples() experimental

Line plot of clone read fraction across multiple samples

plot_sample_vs_sample() experimental

Scatterplot of TCR clone read fraction of clones between two samples

Diversity

calculate_diversity() diversity() experimental

Calculate TCR repertoire diversity metrics

get_all_div_metrics() experimental

Returns all diversity metric options for calculate_diversity()

plot_clonotype_indices() experimental

Stacked bar chart with fractions of reads attributed to the most frequent clonotypes

plot_diversity() experimental

Bar plot of clonal diversity metrics

Export for external tools

create_thimble_df() experimental

Convert paired TCRs to a "thimble" data frame for Stitchr

write_stitchr_tsv() experimental

Write a tab-separated "thimble" text file for use with Stitchr

Well-level data functions

choose_pair_manual() experimental

Choose a partner manually for an input chain using T-SHELL

get_well_subset() experimental

Get well names from numerical rows and columns

get_wells_from_edges() experimental

Get well names from the top left and bottom right wells

load_well_counts_binary() experimental

Load well-level data written to binary format

plot_tshell() experimental

Calculate and plot read fraction correlation across wells (T-SHELL)

write_well_data_to_binary() experimental

Convert individual well .tsv files to faster loading binary format

Data

params

Table of permissible amino acids and V-segments for TCRdist

submat

Substitution penalty matrix for TCRdist amino acids and V-segments

Other