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Explore Data User Guide
Welcome to VDJbase!

The adaptive immune receptor Genotype and Haplotype database

11-Oct-2019 *NEW* - VDJbase is described in Nucleic Acids Research

12-Sep-2019 *NEW* - More datasets and reporting options added! See the Release Notes for more details

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High throughput DNA sequencing technology has been revolutionized in recent years. This technological boom brought with it a wealth of high quality sequencing datasets, produced by groups around the world. An important application of DNA sequencing is exploring adaptive immune receptor repertoires (AIRR), in which many of the immune system’s secrets are hidden.
VDJbase is a publicly available database that offers easy searching of genotype and haplotype data inferred from AIRR-seq datasets. From these data we can explore the variability of the genomic loci of the Ig and TR encoding genes across populations.

View more (User Guide page) >>

What We Offer

Database Search

Use our search page to find open datasets


VDJbase is designed to act as a resource for the scientific community that is interested in exploring the genetic dynamics of the Ig and TR gene loci. The search engine page allows interactive browsing and running database queries. Data is available for bulk download and filtering according to certain metadata parameters. It can also assist in exploring antibody related genetic predisposition to diseases.

Visualizations

Obtain a statistical view on any open dataset by click on the “Export Graph” buttons at the left of the page

VDJbase hosts online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to determine which allele and genes are significantly over-represented in a particular population, in terms of genotype, haplotype and VDJ gene expression. All analysis can be downloaded as friendly visualization graphs. Users can obtain an online interactive graphs which allows to modify parameters according to their interest.

Summary Statistics

View the analysis results of VDJbase data by use “Explore Data” page


“Explore Data” page includes representative analyses of VDJbase. This interface exposes the users to some of the interesting findings revealed by VDJbase.

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Contact Information

We'd love to hear from you

For more information about the database, queries or graphs, browse our User Guide or join the Discussion Forum

Discussion Forum
Faculty of Engineering, Bar-Ilan University, Israel
Birkbeck College, University of London, UK
Share Your Dataset

We believe that public access to our datasets will accelerate interesting discoveries.
Making your data available to other researchers can impact discovery and relevance of your research.

Join us in advancing science, and add your (genoytpe) data to VDJbase.

How do I share data? Please contact us on the Discussion Forum, and we will send you a tutorial.

Release Notes

Summary of recent changes and additions to VDJbase

Date Changes
12-Sep-2019
  • More datasets and reporting options added! See the Explore Data for summary datasets table
  • Added Software version and release information
14-Sep-2019
  • Added Frequently Asked Questions (FAQ). See the User Guide for more details
Versions

Processing versions
* Pipline - v 0.1.0
* Alignment reference - IMGT full - version 4/12/2018
* Alignment tool - IgBLAST v 1.7.0
* Clonotype tool - SCOPer v 0.2.0
* Genotype tool - TIgGER v 0.4.0
* Haplotype tool - RAbHIT v 0.1.2


Visualization versions
* vdjbaseVis - v 0.1.0
* RAbHIT - v 0.1.3


Website version
* Commit ID - NA

*** All codes are available in Bitbucket! ***