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. 2023 Apr 3;39(4):btad126.
doi: 10.1093/bioinformatics/btad126.

RNAget: an API to securely retrieve RNA quantifications

Sean Upchurch  1 , Emilio Palumbo  2 , Jeremy Adams  3 , David Bujold  4 , Guillaume Bourque  4 , Jared Nedzel  5 , Keenan Graham  6 , Meenakshi S Kagda  6 , Pedro Assis  6 , Benjamin Hitz  6 , Emilio Righi  2 , Roderic Guigó  2   7 , Barbara J Wold  1 ; GA4GH RNA-Seq Task Team
Collaborators, Affiliations

RNAget: an API to securely retrieve RNA quantifications

Sean Upchurch et al. Bioinformatics. .

Abstract

Summary: 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.

Availability and implementation: https://ga4gh-rnaseq.github.io/schema/docs/index.html.

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Figures

Figure 1. Schematic of RNAget protocol
Figure 1. Schematic of RNAget protocol
See this image and copyright information in PMC

References

    1. Birney E, Vamathevan J, Goodhand P. Genomics in healthcare: GA4GH looks to 2022. bioRxiv 203554. 2017.
    1. Bujold D, Morais D, Gauthier C. et al. The International Human Epigenome Consortium data portal. Cell Syst 2016;3:496–9.e2. - PubMed
    1. Haque A, Engel J, Teichmann SA. et al. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med 2017;9:75. - PMC - PubMed
    1. Mortazavi A, Williams B, McCue K. et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621–8. - PubMed
    1. Rehm HL, Page AJ, Smith L. et al. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics 2021;1:100029. - PMC - PubMed

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