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immuneSIM (version 0.8.7)

Tunable Simulation of B- And T-Cell Receptor Repertoires

Description

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 ).

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Version

Install

install.packages('immuneSIM')

Monthly Downloads

185

Version

0.8.7

License

GPL-3

Maintainer

C<c3><a9>dric R. Weber

Last Published

September 27th, 2019

Functions in immuneSIM (0.8.7)

shm_event_reconstruction

Decodes immuneSIM repertoire shm_events column.
list_germline_genes_allele_01

Collection of germline genes and frequencies
codon_replacement_reconstruction

Decodes immuneSIM repertoire codon replacements events.
load_insdel_data

Loads full insertion/deletion data from GitHub
one_spot_df

One Spot
motif_implantation

Implant random or predefined motifs into CDR3
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)
immuneSIM

Simulates an immune repertoire based on user-defined parameters
insertions_and_deletion_lengths_df

Dataframe containing insertion sequences and deletion lengths
gen_code

Translation dictionary amino acid <-> nucleotide codon
combine_into_paired

Generates a dataframe from separate heavy and light or beta and alpha chain dataframes
length_dist_simulation

Vector containing VDJ length distributions
codon_replacement

Replaces codons with synonymous codons
hotspot_df

Hotspot dataframe for SHM
list_example_repertoires

Example repertoires
hub_seqs_exclusion

Deletes top hub sequences from repertoire, changing the network architecture.