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

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 complem...

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Detalles Bibliográficos
Autores principales: Wilks, Christopher, Zheng, Shijie C., Chen, Feng Yong, Charles, Rone, Solomon, Brad, Ling, Jonathan P., Imada, Eddie Luidy, Zhang, David, Joseph, Lance, Leek, Jeffrey T., Jaffe, Andrew E., Nellore, Abhinav, Collado-Torres, Leonardo, Hansen, Kasper D., Langmead, Ben
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8628444/
https://www.ncbi.nlm.nih.gov/pubmed/34844637
http://dx.doi.org/10.1186/s13059-021-02533-6
Descripción
Sumario: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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02533-6).