{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T12:02:24Z","timestamp":1753876944951,"version":"3.41.2"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T00:00:00Z","timestamp":1746662400000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM088342","R01GM117624","U01CA233074","P30CA016520-47S3","R01CA287673","U24CA232979","U24CA274159"],"award-info":[{"award-number":["R01GM088342","R01GM117624","U01CA233074","P30CA016520-47S3","R01CA287673","U24CA232979","U24CA274159"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Although gene expression analysis pipelines are often a standard part of bioinformatics analysis, with many publicly available cloud workflows, cloud-based alternative splicing analysis tools remain limited. Our lab released rMATS in 2014 and has continuously maintained it, providing a fast and versatile solution for quantifying alternative splicing from RNA sequencing (RNA-seq) data. Here, we present rMATS-cloud, a portable version of the rMATS workflow that can be run in virtually any cloud environment suited for biomedical research. We compared the time and cost of running rMATS-cloud with two RNA-seq datasets on three different platforms (Cavatica, Terra, and Seqera). Our findings demonstrate that rMATS-cloud handles RNA-seq datasets with thousands of samples, and therefore is ideally suited for the storage capacities of many cloud data repositories. rMATS-cloud is available at https:\/\/dockstore.org\/workflows\/github.com\/Xinglab\/rmats-turbo\/rmats-turbo-cwl, https:\/\/dockstore.org\/workflows\/github.com\/Xinglab\/rmats-turbo\/rmats-turbo-wdl, and https:\/\/dockstore.org\/workflows\/github.com\/Xinglab\/rmats-turbo\/rmats-turbo-nextflow.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf036","type":"journal-article","created":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T19:03:30Z","timestamp":1746731010000},"source":"Crossref","is-referenced-by-count":0,"title":["rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2590-3594","authenticated-orcid":false,"given":"Jenea I","family":"Adams","sequence":"first","affiliation":[{"name":"Genomics and Computational Biology Graduate Group, University of Pennsylvania , Philadelphia, PA 19104,","place":["USA"]},{"name":"Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2160-1820","authenticated-orcid":false,"given":"Eric","family":"Kutschera","sequence":"additional","affiliation":[{"name":"Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4090-5539","authenticated-orcid":false,"given":"Qiang","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3008-3375","authenticated-orcid":false,"given":"Chun-Jie","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1456-5099","authenticated-orcid":false,"given":"Qian","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1437-0147","authenticated-orcid":false,"given":"Kathryn","family":"Kadash-Edmondson","sequence":"additional","affiliation":[{"name":"Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6351-2941","authenticated-orcid":false,"given":"Song","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9257-7613","authenticated-orcid":false,"given":"Yi","family":"Xing","sequence":"additional","affiliation":[{"name":"Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104,","place":["USA"]},{"name":"Department of Pathology and Laboratory Medicine, University of Pennsylvania , Philadelphia, PA 19104,","place":["USA"]},{"name":"Department of Biomedical and Health Informatics, The Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,4,26]]},"reference":[{"key":"2025071112313432300_qzaf036-B1","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1073\/pnas.1525084113","article-title":"Discovery of RNA splicing and genes in pieces","volume":"113","author":"Berk","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025071112313432300_qzaf036-B2","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1038\/s41576-022-00514-4","article-title":"Alternative splicing as a source of phenotypic diversity","volume":"23","author":"Wright","year":"2022","journal-title":"Nat Rev Genet"},{"key":"2025071112313432300_qzaf036-B3","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/s41596-023-00944-2","article-title":"rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data","volume":"19","author":"Wang","year":"2024","journal-title":"Nat Protoc"},{"key":"2025071112313432300_qzaf036-B4","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025071112313432300_qzaf036-B5","first-page":"1379","article-title":"Full-stack genomics pipelining with GATK4 + WDL + Cromwell","volume":"6","author":"Voss","year":"2017","journal-title":"F1000Res"},{"key":"2025071112313432300_qzaf036-B6","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1145\/3486897","article-title":"Methods included: standardizing computational reuse and portability with the Common Workflow Language","volume":"65","author":"Crusoe","year":"2022","journal-title":"Commun ACM"},{"key":"2025071112313432300_qzaf036-B7","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2025071112313432300_qzaf036-B8","doi-asserted-by":"crossref","first-page":"e3\u20136","DOI":"10.1158\/0008-5472.CAN-17-0387","article-title":"The Cancer Genomics Cloud: collaborative, reproducible, and democratized\u2014a new paradigm in large-scale computational research","volume":"77","author":"Lau","year":"2017","journal-title":"Cancer Res"},{"key":"2025071112313432300_qzaf036-B9","doi-asserted-by":"crossref","first-page":"W624","DOI":"10.1093\/nar\/gkab346","article-title":"The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols","volume":"49","author":"Yuen","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025071112313432300_qzaf036-B10","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/s41592-019-0351-9","article-title":"Deep-learning augmented RNA-seq analysis of transcript splicing","volume":"16","author":"Zhang","year":"2019","journal-title":"Nat Methods"},{"key":"2025071112313432300_qzaf036-B11","doi-asserted-by":"crossref","first-page":"e29","DOI":"10.1093\/nar\/gkac1260","article-title":"MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data","volume":"51","author":"Wen","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025071112313432300_qzaf036-B12","doi-asserted-by":"crossref","first-page":"6760","DOI":"10.1016\/j.cell.2024.09.001","article-title":"Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues","volume":"187","author":"Bai","year":"2024","journal-title":"Cell"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gpb\/advance-article-pdf\/doi\/10.1093\/gpbjnl\/qzaf036\/63129281\/qzaf036.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/23\/3\/qzaf036\/63129281\/qzaf036.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/23\/3\/qzaf036\/63129281\/qzaf036.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T16:31:40Z","timestamp":1752251500000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/doi\/10.1093\/gpbjnl\/qzaf036\/8127209"}},"subtitle":[],"editor":[{"given":"Ming","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,4,26]]},"references-count":12,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,7,11]]}},"URL":"https:\/\/doi.org\/10.1093\/gpbjnl\/qzaf036","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"type":"print","value":"1672-0229"},{"type":"electronic","value":"2210-3244"}],"subject":[],"published-other":{"date-parts":[[2025,6]]},"published":{"date-parts":[[2025,4,26]]},"article-number":"qzaf036"}}