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 a...

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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Biology (General) QH301-705.5 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/8ffd406a24644e9286dbf6b7448b3e96
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spelling	oai:doaj.org-article:8ffd406a24644e9286dbf6b7448b3e962021-12-05T12:25:35Zrecount3: summaries and queries for large-scale RNA-seq expression and splicing10.1186/s13059-021-02533-61474-760Xhttps://doaj.org/article/8ffd406a24644e9286dbf6b7448b3e962021-11-01T00:00:00Zhttps://doi.org/10.1186/s13059-021-02533-6https://doaj.org/toc/1474-760XAbstract 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 .Christopher WilksShijie C. ZhengFeng Yong ChenRone CharlesBrad SolomonJonathan P. LingEddie Luidy ImadaDavid ZhangLance JosephJeffrey T. LeekAndrew E. JaffeAbhinav NelloreLeonardo Collado-TorresKasper D. HansenBen LangmeadBMCarticleBiology (General)QH301-705.5GeneticsQH426-470ENGenome Biology, Vol 22, Iss 1, Pp 1-40 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5 Genetics QH426-470
spellingShingle	Biology (General) QH301-705.5 Genetics QH426-470 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 recount3: summaries and queries for large-scale RNA-seq expression and splicing
description	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 .
format	article
author	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
author_facet	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
author_sort	Christopher Wilks
title	recount3: summaries and queries for large-scale RNA-seq expression and splicing
title_short	recount3: summaries and queries for large-scale RNA-seq expression and splicing
title_full	recount3: summaries and queries for large-scale RNA-seq expression and splicing
title_fullStr	recount3: summaries and queries for large-scale RNA-seq expression and splicing
title_full_unstemmed	recount3: summaries and queries for large-scale RNA-seq expression and splicing
title_sort	recount3: summaries and queries for large-scale rna-seq expression and splicing
publisher	BMC
publishDate	2021
url	https://doaj.org/article/8ffd406a24644e9286dbf6b7448b3e96
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recount3: summaries and queries for large-scale RNA-seq expression and splicing

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