As of December 7th, 2022, we are happy to announce the release of iReceptor v4.0. This release consists of two key enhancements:
- support for the recently released version 1.4 of the AIRR Community Standards (including Single-cell support), and
- the release of a new, integrated analysis capability.
Single-cell data available through the iReceptor Platform
Single-cell RNAseq data is becoming increasingly important in our understanding of the complex evolution of the immune system. Recognizing this importance, the AIRR Community recently released version 1.4 of the AIRR Standards, including a standard for storing and querying sc-RNAseq data.
The iReceptor v4.0 release includes a full implementation of the recently released AIRR v1.4 Clone, Cell, and Gene Expression (GEX) data standards. This includes support for the curation, storing, and searching of these data in the iReceptor Turnkey repository, making it possible to store these data in the AIRR Data Commons (ADC). The iReceptor Turnkey repository implements the AIRR Data Commons query API (ADC API) making it possible for researchers to find and download such data from the ADC. Working with iReceptor Plus industry partner 10X Genomics, we provide a mechanism to load the output of the 10X cellranger VDJ pipeline into an iReceptor Turnkey repository.
The iReceptor Gateway utilizes the ADC API to search repositories in the ADC, making it possible to find, access and reuse such data (FAIR). The current Rearrangement data discovery workflow has been extended in v4.0 of the iReceptor Gateway to also support Clone, and Cell workflows. Users can perform study metadata searches to find studies of interest, with the ability to differentiate studies with Rearrangement, Clone, and Cell/GEX data. Once data of interest is discovered, Rearrangement, Clone, and Cell features can also be searched to further refine data of interest. For documentation on how to access these new capabilities, please refer to the Data Discovery Workflow documentation.
We are also pleased to announce the first Single-cell + Gene Expression data set available in the AIRR Data Commons. The data from Yost et al. “Clonal replacement of tumor-specific T cells following PD-1 blockade” has been loaded into the iReceptor Public Archive (IPA) repository and this study is available to search and download through the iReceptor Gateway.
Integrated analysis now available in the iReceptor Platform
The iReceptor v4.0 release has also added the ability to perform advanced computational analyses of data discovered through the iReceptor Gateway. Commonly used analysis tools developed by the community (e.g. Immunarch, Conga, CellTypist) have been integrated into the iReceptor Gateway, making it possible to run these tools within the platform without having to download data to the users desktop. Supported analysis tools can be run on any data that is found in the AIRR Data Commons. For more information on how to use this new capability, please refer to the Data Analysis and Jobs section of the documentation.
For more information on the impacts of the upgrade on the data stored in the iReceptor repositories and the AIRR Data Commons please refer to the iReceptor v4.0 Data Provenance page.