Man pages for immuneSIM
Tunable Simulation of B- And T-Cell Receptor Repertoires

codon_replacementReplaces codons with synonymous codons
codon_replacement_reconstructionDecodes immuneSIM repertoire codon replacements events.
combine_into_pairedGenerates a dataframe from separate heavy and light or beta...
gen_codeTranslation dictionary amino acid <-> nucleotide codon
hotspot_dfHotspot dataframe for SHM
hub_seqs_exclusionDeletes top hub sequences from repertoire, changing the...
immuneSIMSimulates an immune repertoire based on user-defined...
insertions_and_deletion_lengths_dfDataframe containing insertion sequences and deletion lengths
length_dist_simulationVector containing VDJ length distributions
list_example_repertoiresExample repertoires
list_germline_genes_allele_01Collection of germline genes and frequencies
load_insdel_dataLoads full insertion/deletion data from GitHub
motif_implantationImplant random or predefined motifs into CDR3
one_spot_dfOne Spot
plot_repertoire_A_vs_BComparative plots of main repertoire features of two input...
plot_report_repertoirePlots main repertoire features (length distribution,amino...
shm_event_reconstructionDecodes immuneSIM repertoire shm_events column.
immuneSIM documentation built on Sept. 27, 2019, 5:02 p.m.