{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T12:24:21Z","timestamp":1772627061901,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2017,10,23]],"date-time":"2017-10-23T00:00:00Z","timestamp":1508716800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Short reads sequencing technology has been used for more than a decade now. However, the analysis of RNAseq and ChIPseq data is still computational demanding and the simple access to raw data does not guarantee results reproducibility between laboratories. To address these two aspects, we developed SeqBox, a cheap, efficient and reproducible RNAseq\/ChIPseq hardware\/software solution based on NUC6I7KYK mini-PC (an Intel consumer game computer with a fast processor and a high performance SSD disk), and Docker container platform. In SeqBox the analysis of RNAseq and ChIPseq data is supported by a friendly GUI. This allows access to fast and reproducible analysis also to scientists with\/without scripting experience.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Docker container images, docker4seq package and the GUI are available at http:\/\/www.bioinformatica.unito.it\/reproducibile.bioinformatics.html.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx674","type":"journal-article","created":{"date-parts":[[2017,10,19]],"date-time":"2017-10-19T19:10:03Z","timestamp":1508440203000},"page":"871-872","source":"Crossref","is-referenced-by-count":29,"title":["SeqBox: RNAseq\/ChIPseq reproducible analysis on a consumer game computer"],"prefix":"10.1093","volume":"34","author":[{"given":"Marco","family":"Beccuti","sequence":"first","affiliation":[{"name":"Department of Computer Sciences, University of Torino, Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"Cordero","sequence":"additional","affiliation":[{"name":"Department of Computer Sciences, University of Torino, Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maddalena","family":"Arigoni","sequence":"additional","affiliation":[{"name":"Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riccardo","family":"Panero","sequence":"additional","affiliation":[{"name":"Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elvio G","family":"Amparore","sequence":"additional","affiliation":[{"name":"Department of Computer Sciences, University of Torino, Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susanna","family":"Donatelli","sequence":"additional","affiliation":[{"name":"Department of Computer Sciences, University of Torino, Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raffaele A","family":"Calogero","sequence":"additional","affiliation":[{"name":"Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,10,23]]},"reference":[{"key":"2023012712383046800_btx674-B1","doi-asserted-by":"crossref","first-page":"e31630","DOI":"10.1371\/journal.pone.0031630","article-title":"Optimizing a massive parallel sequencing workflow for quantitative miRNA expression analysis","volume":"7","author":"Cordero","year":"2012","journal-title":"PLoS One"},{"key":"2023012712383046800_btx674-B2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712383046800_btx674-B3","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/1471-2105-15-182","article-title":"Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads","volume":"15","author":"Jiang","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023012712383046800_btx674-B4","doi-asserted-by":"crossref","first-page":"323.","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012712383046800_btx674-B5","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012712383046800_btx674-B6","doi-asserted-by":"crossref","first-page":"550.","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023012712383046800_btx674-B7","author":"Wong"},{"key":"2023012712383046800_btx674-B8","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1007\/978-1-4939-0512-6_5","article-title":"Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells","volume":"1150","author":"Xu","year":"2014","journal-title":"Methods Mol. 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