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

doi:10.1186/s13059-021-02533-6

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

Genome Biol. 2021 Nov 29;22(1):323. doi: 10.1186/s13059-021-02533-6.

Authors

Christopher Wilks¹, Shijie C Zheng², Feng Yong Chen³, Rone Charles¹, Brad Solomon⁴, Jonathan P Ling⁵, Eddie Luidy Imada⁶, David Zhang⁷, Lance Joseph³, Jeffrey T Leek², Andrew E Jaffe^{2

8

9

10}, Abhinav Nellore^{11

12}, Leonardo Collado-Torres⁸, Kasper D Hansen^{13

14}, Ben Langmead¹⁵

Affiliations

¹ Department of Computer Science, Johns Hopkins University, Baltimore, USA.
² Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA.
³ Johns Hopkins University, Baltimore, USA.
⁴ Thomas M. Siebel Center for Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
⁵ Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA.
⁶ Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
⁷ Institute of Child Health, University College London (UCL), London, UK.
⁸ Lieber Institute for Brain Development, Baltimore, USA.
⁹ Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA.
¹⁰ Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA.
¹¹ Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
¹² Department of Surgery, Oregon Health & Science University, Portland, OR, USA.
¹³ Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA. khansen@jhsph.edu.
¹⁴ Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA. khansen@jhsph.edu.
¹⁵ Department of Computer Science, Johns Hopkins University, Baltimore, USA. langmea@cs.jhu.edu.

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 .

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Sequence
Computational Biology / methods
Exons
Gene Expression Regulation
High-Throughput Nucleotide Sequencing
Humans
Mice
RNA / genetics*
RNA Splicing*
RNA-Seq / methods*
Sequence Analysis, RNA / methods
Software

Substances

RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding