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. |