{"repo":"antigenomics/vdjdb-db","free":true,"listed":false,"github":"https://github.com/antigenomics/vdjdb-db","clone":"git clone https://github.com/antigenomics/vdjdb-db.git","description":"Git-based antigen specificity database storage & management.","language":"Python","stars":155,"topics":["bioinformatics","immunology","database","antigen","t-cell","binding","hla","mhc","receptor","recognition"],"license":"AGPL-3.0","category":"databases-storage","readme_excerpt":"VDJDB: A curated database of T-cell receptor sequences of known antigen specificity The primary goal of VDJdb is to facilitate access to existing information on T-cell receptor antigen specificities, i.e. the ability to recognize certain epitopes in certain MHC contexts. Our mission is to both aggregate the scarce TCR specificity information available so far and to create a curated repository to store such data. In addition to routine database updates providing the most up-to-date information, we make our best to ensure data consistency and fight irregularities in TCR specificity reporting with a complex database validation scheme: We take into account all available information on experimental setup used to identify antigen-specific TCR sequences and assign a single confidence score to highligh most reliable records at the database generation stage. Each database record is also automatically checked against a database of V/J segment germline sequences to ensure standardized and consistent reporting of V-J junctions and CDR3 sequences that define T-cell clones. This repository hosts the submissions to database and scripts to check, fix and build the database itself. To build database directly from submissions, go to src directory and run groovy -cp . BuildDatabase.groovy script (requires Groovy). To query the database for your immune repertoire sample(s) use the vdjmatch software. A web-based GUI for the database can be found in VDJdb-web repository. Citing Please cite the dat","default_branch":null,"files":null,"tree":[],"storefront":"/r/antigenomics","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/antigenomics/vdjdb-db/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}