Tunable Simulation of B- And T-Cell Receptor Repertoires
Replaces codons with synonymous codons
Decodes immuneSIM repertoire codon replacements events.
Generates a dataframe from separate heavy and light or beta and alpha ...
Translation dictionary amino acid <-> nucleotide codon
Hotspot dataframe for SHM
Deletes top hub sequences from repertoire, changing the network archit...
Simulates an immune repertoire based on user-defined parameters
Dataframe containing insertion sequences and deletion lengths
Vector containing VDJ length distributions
Example repertoires
Collection of germline genes and frequencies
Loads full insertion/deletion data from GitHub
Implant random or predefined motifs into CDR3
One Spot
Comparative plots of main repertoire features of two input repertoires...
Plots main repertoire features (length distribution,amino acid frequen...
Decodes immuneSIM repertoire shm_events column.
Simulate full B-cell and T-cell receptor repertoires using an in silico recombination process that includes a wide variety of tunable parameters to introduce noise and biases. Additional post-simulation modification functions allow the user to implant motifs or codon biases as well as remodeling sequence similarity architecture. The output repertoires contain records of all relevant repertoire dimensions and can be analyzed using provided repertoire analysis functions. Preprint is available at bioRxiv (Weber et al., 2019 <doi:10.1101/759795>).