antigen_db: Antigen DB

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Antigen DB

Description

The database is created from flat file versions of IEDB, McPAS-TCR, and VdjDB slim in that order and generates an RDA file of all T-cells and B-cells recorded to show antigenic specificity in these three databases. This is a script for internal use and will be run once every six months to update the databases.

Usage

antigen_db

Format

antigen_db

A tibble with 320,786 rows and 16 columns:

tra_cdr3_aa

T-cell receptor alpha chain amino acid sequence

gene

Antigen gene/protein name

epitope

Antigen epitope sequence/target

pathology

Pathology associated with epitope

antigen

Name of antigen

tra_v_call

T-cell receptor alpha chain V gene

tra_j_call

T-cell receptor alpha chain J gene

mhc_allele

MHC allele associated with the epitope

reference

Reference for known antigenic specificity

score

Confidence of the antigenic specificity

cell_type

Immune cell type

source

Database name

trb_cdr3_aa

T-cell receptor beta chain amino acid sequence

trb_v_call

T-cell receptor beta chain V gene

trb_j_call

T-cell receptor beta chain J gene

Species

Species

Source

The flat files for this function can be downloaded at the following links:

1. IEDB: https://www.iedb.org/downloader.php?file_name=doc/receptor_full_v3.zip

2. McPAS-TCR: http://friedmanlab.weizmann.ac.il/McPAS-TCR/

3. VdjDB: https://github.com/antigenomics/vdjdb-db/releases Note: Here the vdjdb.slim.txt is used as the input Note: The order of the input matters, please provide the flat file paths in this order IEDB, McPAS-TCR, VdjDB.

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.