RNAget: an API to securely retrieve RNA quantifications

Creators: Upchurch, Sean; Palumbo, Emilio; Adams, Jeremy; Bujold, David; Bourque, Guillaume; Nedzel, Jared; Graham, Keenan; Kagda, Meenakshi S.; Assis, Pedro; Hitz, Benjamin; Righi, Emilio; Guigó, Roderic; Wold, Barbara J.; GA4GH RNA-Seq Task Team

Abstract

Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in matrix form. RNAget provides for slicing matrices to extract desired subsets of data and is applicable to all expression matrix-format data, including RNA sequencing and microarrays. Further, it generalizes to quantification matrices of other sequence-based genomics such as ATAC-seq and ChIP-seq.

Additional Information

© The Author(s) 2023. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. RNAget was created by the GA4GH RNA-seq task team. We gratefully acknowledge the support of the GA4GH secretariat and the essential advice and input from GA4GH reviewers Laura Clarke, Mark Diekhans, David Glazer, Sten Linnarsson and Andy Yates. Collaborators: GA4GH RNA-seq Task Team: Jeremy Adams Alvis Brazma, David Bujold Julia Burchard, Joe Capka, Michael Cherry, Laura Clarke, Brian Craft, Manolis Dermitzakis, Mark Diekhans, John Dursi, Michael Sean Fitzsimons, Zac Flaming, Romina Garrido, Alfred Gil, Paul Godden, Matt Green, Roderic Guigo Mitch Guttman, Brian Haas, Max Haeussler, Benjamin Hitz Bo Li, Sten Linnarsson, Adam Lipski, David Liu, Simonne Longerich, David Lougheed, Jonathan Manning, John Marioni, Christopher Meyer, Stephen Montgomery, Alyssa Morrow, Alfonso Munoz-Power Fuentes, Jared Nedzel David Nguyen, Kevin Osborn, Francis Ouellette, Emilio Palumbo Irene Papatheodorou, Dmitri Pervouchine, Arun Ramani, Jordi Rambla, Bashir Sadjad, David Steinberg, Jeremiah Talkar, Timothy Tickle, Kathy Tzeng, Sean Upchurch Saman Vaisipour, Sean Watford, Barbara Wold Zhenyu Zhang, and Jing Zhu. This work was supported by Genome Canada/Génome Québec [249333 to G.B.]; Canadian Institutes of Health Research [CEE-151618 to G.B.]; European Regional Development Fund (FEDER) [IMP/00019 and VEIS-001-P-001647]; Spanish Ministry of Science and Innovation to the EMBL partnership; Centro de Excelencia Severo Ochoa; CERCA Programme/Generalitat de Catalunya; the National Institutes of Health [OT2 OD030161-01, U54HG006998 to B.J.W., UM1HG009443 to B.J.W., and HG012077 to B.J.W.]; Beckman Foundation to [B.J.W.]; Bren Foundation to [B.J.W.]; and Braun Trust to [B.J.W.]. RNAget was created by the GA4GH RNA-seq task team. We gratefully acknowledge the support of the GA4GH secretariat and the essential advice and input from GA4GH reviewers Laura Clarke, Mark Diekhans, David Glazer, Sten Linnarsson and Andy Yates. Collaborators: GA4GH RNA-seq Task Team: Jeremy Adams Alvis Brazma, David Bujold Julia Burchard, Joe Capka, Michael Cherry, Laura Clarke, Brian Craft, Manolis Dermitzakis, Mark Diekhans, John Dursi, Michael Sean Fitzsimons, Zac Flaming, Romina Garrido, Alfred Gil, Paul Godden, Matt Green, Roderic Guigo Mitch Guttman, Brian Haas, Max Haeussler, Benjamin Hitz Bo Li, Sten Linnarsson, Adam Lipski, David Liu, Simonne Longerich, David Lougheed, Jonathan Manning, John Marioni, Christopher Meyer, Stephen Montgomery, Alyssa Morrow, Alfonso Munoz-Power Fuentes, Jared Nedzel David Nguyen, Kevin Osborn, Francis Ouellette, Emilio Palumbo Irene Papatheodorou, Dmitri Pervouchine, Arun Ramani, Jordi Rambla, Bashir Sadjad, David Steinberg, Jeremiah Talkar, Timothy Tickle, Kathy Tzeng, Sean Upchurch Saman Vaisipour, Sean Watford, Barbara Wold Zhenyu Zhang, and Jing Zhu. Conflict of interest: None declared.

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