Category: VDJbase_Help

Using the VDJbase REST API

The REST API allows you to access VDJbase programatically, which can be useful if you want to incorporate data into your own systems, and keep it up-to-date. All communication between the VDJbase client in the browser and the VDJbase server is via the API: any data you see in the browser has been provided over… Continue reading Using the VDJbase REST API

Genomic data in VDJbase

Genomic data is organised into ‘genomic sets’: typically a genomic set will contain data relating to a single locus of a species. At the moment, VDJbase holds genomic data for Rhesus Macaque but not for Human: when entering the Genomic pages, be sure to select Rhesus Macaque as the species at the top left hand… Continue reading Genomic data in VDJbase

Downloading data

Select the sample or allele data that you would like to download by using the filters, and press Download. For sample data, ‘csv’ will download a csv file with the information displayed on the Sample page, while ‘zip’ will download all files and reports for the selected samples. For alleles, ‘Gene information’ provides the information… Continue reading Downloading data

Analysing data

To analyse data using VDJbase’s built-in reports, first select the saimples you are interested in by using the filters, then go to the Reports page. This will display the analyses available for your selection. Note that many analyses will only run with a single dataset selected. If you do not set any filters, the analysis… Continue reading Analysing data

Searching for AIRR-Seq records

You can display multiple data sets for the same species where these are available: first select the species of interest, then check the datasets for that species that you wish to search. Usually these will correspond to individual loci. VDJbase uses an Excel-style approach to searching and browsing data: click on the little triangle to… Continue reading Searching for AIRR-Seq records

AIRR-Seq data: Allele Names

The Germline Genes page lists all alleles discovered in the data set(s). The Appearances column counts the number of individuals in which each allele is found. You can click on a number in the Appearances column to view a list of samples containing instances of the allele. Note that the number of samples may not… Continue reading AIRR-Seq data: Allele Names

AIRR-Seq data: Sample Names

VDJbase uses a structured name such as P1_I41_S1 to refer to each sample. The numbers following P, I and S are allocated serially by VDJbase. P indicates the project number. You can see a list of projects on the Explore Data page. I is followed by a number identifying the individual within that project, and… Continue reading AIRR-Seq data: Sample Names

Citing VDJbase

If you use VDJbase in your work, please cite our paper: Aviv Omer, Or Shemesh, Ayelet Peres, Pazit Polak, Adrian J Shepherd, Corey T Watson, Scott D Boyd, Andrew M Collins, William Lees, Gur Yaari, VDJbase: an adaptive immune receptor genotype and haplotype database, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D1051–D1056,… Continue reading Citing VDJbase