Tunable Simulation of B- And T-Cell Receptor Repertoires

Documentation for package ‘immuneSIM’ version 0.8.7

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.