Work

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

Year: 2021

Type: article

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 .

Source: Genome biology

DOI: 10.1186/s13059-021-02533-6

Authors: 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

Institutions: Johns Hopkins University, University of Illinois Urbana-Champaign, Johns Hopkins Medicine, Weill Cornell Medicine, University College London, Lieber Institute for Brain Development, Oregon Health & Science University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $4,890

Funders: National Science Foundation, University of Texas at Austin, Maryland Advanced Research Computing Center, Department of Mechanical Engineering, University of Texas at Austin, Medical Research Council, National Institute of General Medical Sciences, Office of Advanced Cyberinfrastructure

Awards: G3226045097, XSEDE 2.0: Integrating, Enabling and Enhancing National Cyberinfrastructure with Expanding Community Involvement, G4875486994, Using transcriptomics to transform the diagnosis and understanding of inherited adult neurological disorders, Hardening and Scaling Core Genomics Software, G7400298905, Analysis of genomics datasets at a massive scale, Methods for sequencing data analysis and archive-scale data science

OpenAlex ID: W3216633781

FWCI: 12.68

Cites: 65

Cited by: 269

Related to: 10