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

Wilks, C.; Zheng, S. C.; Chen, F. Y.; Charles, R.; Solomon, B.; Ling, J. P.; Imada, E. L.; Zhang, D.; Joseph, L.; Leek, J. T.; Jaffe, A. E.; Nellore, A.; Collado-Torres, L.; Hansen, K. D.; Langmead, B.

doi:10.1101/2021.05.21.445138

bioRxiv · 10.1101/2021.05.21.445138

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

Wilks, C.·Zheng, S. C.·Chen, F. Y.·Charles, R.·Solomon, B.·Ling, J. P.·Imada, E. L.·Zhang, D.·Joseph, L.·Leek, J. T.·Jaffe, A. E.·Nellore, A.·Collado-Torres, L.·Hansen, K. D.·Langmead, B.

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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.

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Wilks, C., Zheng, S. C., Chen, F. Y., Charles, R., Solomon, B., Ling, J. P., Imada, E. L., Zhang, D., Joseph, L., Leek, J. T., Jaffe, A. E., Nellore, A., Collado-Torres, L., Hansen, K. D., Langmead, B.. 2021-05-23. recount3: summaries and queries for large-scale RNA-seq expression and splicing. https://doi.org/10.1101/2021.05.21.445138

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