# Tunable Simulation of B- And T-Cell Receptor Repertoires

## Documentation for package ‘immuneSIM’ version 0.8.7

- DESCRIPTION file.

## Help Pages

codon_replacement | Replaces codons with synonymous codons
codon_replacement_reconstruction | Decodes immuneSIM repertoire codon replacements events.
combine_into_paired | Generates a dataframe from separate heavy and light or beta and alpha chain dataframes
gen_code | Translation dictionary amino acid <-> nucleotide codon
hotspot_df | Hotspot dataframe for SHM
hub_seqs_exclusion | Deletes top hub sequences from repertoire, changing the network architecture.
immuneSIM | Simulates an immune repertoire based on user-defined parameters
insertions_and_deletion_lengths_df | Dataframe containing insertion sequences and deletion lengths
length_dist_simulation | Vector containing VDJ length distributions
list_example_repertoires | Example repertoires
list_germline_genes_allele_01 | Collection of germline genes and frequencies
load_insdel_data | Loads full insertion/deletion data from GitHub
motif_implantation | Implant random or predefined motifs into CDR3
one_spot_df | One Spot
plot_repertoire_A_vs_B | Comparative plots of main repertoire features of two input repertoires (length distribution, amino acid frequency, VDJ usage, kmer occurrence)
plot_report_repertoire | Plots main repertoire features (length distribution,amino acid frequencies and VDJ usage)
shm_event_reconstruction | Decodes immuneSIM repertoire shm_events column.