vdjdb: vdjdb slim dataset

In xizhihui/BTCR: Simple Stats and Plots for BCR and TCR

Description

A data frame from vdjdb.slim.txt

Usage

vdjdb

Format

A data frame with 16 columns

gene

TCR chain: alpha or beta

cdr3

TCR complementarity determining region 3 (CDR3) amino acid sequence

species

TCR parent species

antigen.epitope

Amino acid sequence of the epitope

antigen.gene

Representative parent gene of the epitope

antigen.species

Representative parent species of the epitope

complex.id

TCR alpha and beta chain records having the same complex identifier belong to the same T-cell clone

v.segm

TCR Variable segment allele

j.segm

TCR Joining segment allele

v.end

End of v.segm

j.start

Start of j.segm

mhc.a

First MHC chain allele

mhc.b

Second MHC chain allele (defaults to Beta2Microglobulin for MHC class I)

mhc.class

MHC class MHC class (I or II)

reference.id

Pubmed reference / URL / or submitter details in case unpublished

vdjdb.score

VDJdb confidence score, the higher is the score the more confidence we have in the antigen specificity annotation of a given TCR clonotype/clone. Zero score indicates that there are insufficient method details to draw any conclusion

Source

https://github.com/antigenomics/vdjdb-db

xizhihui/BTCR documentation built on Dec. 23, 2021, 7:10 p.m.