recount3: summaries and queries for large-scale RNA-seq expression and splicing
recount3: summaries and queries for large-scale RNA-seq expression and splicing
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.
Charles Rone、Zheng Shijie C.、Leek Jeffrey T.、Chen Feng Yong、Imada Eddie Luidy、Collado-Torres Leonardo、Jaffe Andrew E.、Zhang David、Hansen Kasper D.、Ling Jonathan P.、Wilks Christopher、Langmead Ben、Joseph Lance、Solomon Brad、Nellore Abhinav
Department of Computer Science, Johns Hopkins UniversityDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public HealthDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public HealthJohns Hopkins UniversityDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineLieber Institute for Brain DevelopmentDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health||Lieber Institute for Brain Development||Department of Genetic Medicine, Johns Hopkins School of Medicine||Department of Mental Health, Johns Hopkins Bloomberg School of Public HealthInstitute of Child Health, University College London (UCL)Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health||Department of Genetic Medicine, Johns Hopkins School of MedicineDepartment of Pathology, Johns Hopkins University School of MedicineDepartment of Computer Science, Johns Hopkins UniversityDepartment of Computer Science, Johns Hopkins UniversityJohns Hopkins UniversityThomas M. Siebel Center for Computer Science, University of Illinois at Urbana-ChampaignDepartment of Biomedical Engineering, Oregon Health & Science University||Department of Surgery, Oregon Health & Science University
生物科学研究方法、生物科学研究技术分子生物学遗传学
Charles Rone,Zheng Shijie C.,Leek Jeffrey T.,Chen Feng Yong,Imada Eddie Luidy,Collado-Torres Leonardo,Jaffe Andrew E.,Zhang David,Hansen Kasper D.,Ling Jonathan P.,Wilks Christopher,Langmead Ben,Joseph Lance,Solomon Brad,Nellore Abhinav.recount3: summaries and queries for large-scale RNA-seq expression and splicing[EB/OL].(2025-03-28)[2025-05-10].https://www.biorxiv.org/content/10.1101/2021.05.21.445138.点此复制
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