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.
