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
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Publicado: BMC 2021
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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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