list_germline_genes_allele_01: Collection of germline genes and frequencies

In immuneSIM: Tunable Simulation of B- And T-Cell Receptor Repertoires

Description

A list containing sublists for species ("hs","mm") which in turn contain sublists for receptors ("ig","tr") which are subset in chains ("h", "k", "l" and "b", "a", respectively). Each entry contains a list of three dataframes ("V","D" and "J") with the major IMGT annotated germline genes including name, sequence based on IMGT and frequencies based on experimental data from DeWitt(2017), Emerson (2017), Greiff (2017) and Madi (2017)

Usage

list_germline_genes_allele_01

Format

A list of lists containing dataframes with up to 126 entries:

gene

name of germline gene

allele

allele number (presently restricted to allele 01)

sequence

nucleotide sequence of germline gene

species

name of species

frequency

Frequencies of germline genes based on experimental data

Source

http://www.imgt.org/vquest/refseqh.html

https://doi.org/10.1371/journal.pone.0160853

https://doi.org/10.1038/ng.3822

https://doi.org/10.1016/j.celrep.2017.04.054

https://doi.org/10.7554/eLife.22057

immuneSIM documentation built on Sept. 27, 2019, 5:02 p.m.