{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T23:45:44Z","timestamp":1722728744985},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2089,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,15]]},"abstract":"Abstract<\/jats:title>\n Summary: We present an R based pipeline, ArrayExpressHTS, for pre-processing, expression estimation and data quality assessment of high-throughput sequencing transcriptional profiling (RNA-seq) datasets. The pipeline starts from raw sequence files and produces standard Bioconductor R objects containing gene or transcript measurements for downstream analysis along with web reports for data quality assessment. It may be run locally on a user's own computer or remotely on a distributed R-cloud farm at the European Bioinformatics Institute. It can be used to analyse user's own datasets or public RNA-seq datasets from the ArrayExpress Archive.<\/jats:p>\n Availability: The R package is available at www.ebi.ac.uk\/tools\/rcloud with online documentation at www.ebi.ac.uk\/Tools\/rwiki\/, also available as supplementary material.<\/jats:p>\n Contact: \u00a0angela.goncalves@ebi.ac.uk<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr012","type":"journal-article","created":{"date-parts":[[2011,1,14]],"date-time":"2011-01-14T04:50:46Z","timestamp":1294980646000},"page":"867-869","source":"Crossref","is-referenced-by-count":46,"title":["A pipeline for RNA-seq data processing and quality assessment"],"prefix":"10.1093","volume":"27","author":[{"given":"Angela","family":"Goncalves","sequence":"first","affiliation":[{"name":"EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK"}]},{"given":"Andrew","family":"Tikhonov","sequence":"additional","affiliation":[{"name":"EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK"}]},{"given":"Alvis","family":"Brazma","sequence":"additional","affiliation":[{"name":"EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK"}]},{"given":"Misha","family":"Kapushesky","sequence":"additional","affiliation":[{"name":"EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK"}]}],"member":"286","published-online":{"date-parts":[[2011,1,13]]},"reference":[{"key":"2023012511552781900_B1","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/nbt.1633","article-title":"Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs","volume":"28","author":"Guttman","year":"2010","journal-title":"Nat. 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