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recount3: summaries and queries for large-scale RNA-seq expression and splicing

View ORCID ProfileChristopher Wilks, View ORCID ProfileShijie C. Zheng, Feng Yong Chen, View ORCID ProfileRone Charles, View ORCID ProfileBrad Solomon, View ORCID ProfileJonathan P. Ling, View ORCID ProfileEddie Luidy Imada, View ORCID ProfileDavid Zhang, View ORCID ProfileLance Joseph, View ORCID ProfileJeffrey T. Leek, View ORCID ProfileAndrew E. Jaffe, View ORCID ProfileAbhinav Nellore, View ORCID ProfileLeonardo Collado-Torres, View ORCID ProfileKasper D. Hansen, View ORCID ProfileBen Langmead
doi: https://doi.org/10.1101/2021.05.21.445138
Christopher Wilks
1Department of Computer Science, Johns Hopkins University, University of Illinois at Urbana-Champaign, Urbana, Illinois
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Shijie C. Zheng
2Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, University of Illinois at Urbana-Champaign, Urbana, Illinois Urbana-Champaign, Urbana, Illinois
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Feng Yong Chen
3Johns Hopkins University, University of Illinois at Urbana-Champaign, Urbana, Illinois
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Rone Charles
1Department of Computer Science, Johns Hopkins University, University of Illinois at Urbana-Champaign, Urbana, Illinois
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Brad Solomon
4Thomas M. Siebel Center for Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois
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Jonathan P. Ling
5Department of Pathology, Johns Hopkins University School of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois
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Eddie Luidy Imada
6Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
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David Zhang
7Institute of Child Health, University College London (UCL), London, UK
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Lance Joseph
3Johns Hopkins University, University of Illinois at Urbana-Champaign, Urbana, Illinois
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Jeffrey T. Leek
2Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, University of Illinois at Urbana-Champaign, Urbana, Illinois Urbana-Champaign, Urbana, Illinois
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Andrew E. Jaffe
2Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, University of Illinois at Urbana-Champaign, Urbana, Illinois Urbana-Champaign, Urbana, Illinois
8Lieber Institute for Brain Development, University College London (UCL), London, UK
9Department of Genetic Medicine, Johns Hopkins School of Medicine, University College London (UCL), London, UK
10Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, University College London (UCL), London, UK
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Abhinav Nellore
11Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
12Department of Surgery, Oregon Health & Science University, Portland, Oregon
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Leonardo Collado-Torres
8Lieber Institute for Brain Development, University College London (UCL), London, UK
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Kasper D. Hansen
2Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, University of Illinois at Urbana-Champaign, Urbana, Illinois Urbana-Champaign, Urbana, Illinois
9Department of Genetic Medicine, Johns Hopkins School of Medicine, University College London (UCL), London, UK
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  • For correspondence: langmea@cs.jhu.edu khansen@jhsph.edu
Ben Langmead
1Department of Computer Science, Johns Hopkins University, University of Illinois at Urbana-Champaign, Urbana, Illinois
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  • For correspondence: langmea@cs.jhu.edu khansen@jhsph.edu
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ABSTRACT

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 23, 2021.
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recount3: summaries and queries for large-scale RNA-seq expression and splicing
Christopher Wilks, Shijie C. Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie Luidy Imada, David Zhang, Lance Joseph, Jeffrey T. Leek, Andrew E. Jaffe, Abhinav Nellore, Leonardo Collado-Torres, Kasper D. Hansen, Ben Langmead
bioRxiv 2021.05.21.445138; doi: https://doi.org/10.1101/2021.05.21.445138
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recount3: summaries and queries for large-scale RNA-seq expression and splicing
Christopher Wilks, Shijie C. Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie Luidy Imada, David Zhang, Lance Joseph, Jeffrey T. Leek, Andrew E. Jaffe, Abhinav Nellore, Leonardo Collado-Torres, Kasper D. Hansen, Ben Langmead
bioRxiv 2021.05.21.445138; doi: https://doi.org/10.1101/2021.05.21.445138

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