IGHV_Epitopes: Net charge usage in CDR3 sequences of T-cell receptor...

In snaketron/test_repo: Differential gene usage in immune repertoires

Description

Data of CDR3 sequence from human T-cells receptors (TRB-chain) downloaded from VDJdb. CDR3 sequences annotated to epitopes in Influenza-A and CMV were selected from different publications, as long as the publication contains at least 100 CDR3 sequences. Each publication is considered as a repertoire (sample).

To compute the net CDR3 sequence charge, we consider the amino acids K, R and H as +1 charged, while D and E as -1 charged. Thus, we computed the net charge of a CDR3 sequence by adding up the individual residue charges.

Usage

data("CDR3_Epitopes")

Format

A data frame with 4 columns: "sample_id", "condition", "gene_name" and "gene_usage_count". The format of the data is suitible to be used as input in IgGeneUsage

gene_name = net charge group

Source

https://vdjdb.cdr3.net/

Examples

data(CDR3_Epitopes)
head(CDR3_Epitopes)

snaketron/test_repo documentation built on Dec. 23, 2021, 3:28 a.m.