{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T20:28:17Z","timestamp":1777926497234,"version":"3.51.4"},"reference-count":12,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2016,6,9]],"date-time":"2016-06-09T00:00:00Z","timestamp":1465430400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    The ribosome profiling technique (Ribo-seq) allows the selective sequencing of translated\u00a0RNA regions. Recently, the analysis of genomic sequences associated to Ribo-seq reads\u00a0has been widely employed to assess their coding potential. These analyses led to the identification\u00a0of differentially translated transcripts under different experimental conditions, and\/or\u00a0ribosome pausing on codon motifs. In the context of the ever-growing need for tools analyzing\u00a0Ribo-seq reads, we have developed \u2018RiboProfiling\u2019, a new Bioconductor open-source\u00a0package. \u2018RiboProfiling\u2019 provides a full pipeline to cover all key steps for the analysis of ribosome\u00a0footprints. This pipeline has been implemented in a single R workflow. The package\u00a0takes an alignment (BAM) file as input and performs ribosome footprint quantification at a\u00a0transcript level. It also identifies footprint accumulation on particular amino acids or multi\u00a0amino-acids motifs. Report summary graphs and data quantification are generated automatically.\u00a0The package facilitates quality assessment and quantification of Ribo-seq experiments. Its\u00a0implementation in Bioconductor enables the modeling and statistical analysis of its output\u00a0through the vast choice of packages available in R. This article illustrates how to identify\u00a0codon-motifs accumulating ribosome footprints, based on data from\n                    <ns4:italic>Escherichia coli<\/ns4:italic>\n                    .\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.8964.1","type":"journal-article","created":{"date-parts":[[2016,6,9]],"date-time":"2016-06-09T13:23:37Z","timestamp":1465478617000},"page":"1309","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":63,"title":["RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing"],"prefix":"10.12688","volume":"5","author":[{"given":"Alexandra","family":"Popa","sequence":"first","affiliation":[]},{"given":"Kevin","family":"Lebrigand","sequence":"additional","affiliation":[]},{"given":"Agnes","family":"Paquet","sequence":"additional","affiliation":[]},{"given":"Nicolas","family":"Nottet","sequence":"additional","affiliation":[]},{"given":"Karine","family":"Robbe-Sermesant","sequence":"additional","affiliation":[]},{"given":"Rainer","family":"Waldmann","sequence":"additional","affiliation":[]},{"given":"Pascal","family":"Barbry","sequence":"additional","affiliation":[]}],"member":"2560","published-online":{"date-parts":[[2016,6,9]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"981-993","DOI":"10.1002\/embj.201488411","article-title":"Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.","volume":"33","author":"A Bazzini","year":"2014","journal-title":"EMBO 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O\u2019Connor","year":"2015","journal-title":"bioRxiv."},{"key":"ref-9","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.54567","article-title":"scriptWoolstenhulme_Defp2.R.","author":"A Popa","year":"2016","journal-title":"Zenodo."},{"key":"ref-10","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1186\/s12864-016-2384-0","article-title":"Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells.","volume":"17","author":"A Popa","year":"2016","journal-title":"BMC Genomics."},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"7200","DOI":"10.1038\/ncomms8200","article-title":"Translational regulation shapes the molecular landscape of complex disease phenotypes.","volume":"6","author":"S Schafer","year":"2015","journal-title":"Nat Commun."},{"key":"ref-12","doi-asserted-by":"publisher","first-page":"13-21","DOI":"10.1016\/j.celrep.2015.03.014","article-title":"High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP.","volume":"11","author":"C Woolstenhulme","year":"2015","journal-title":"Cell Rep."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/5-1309\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/5-1309\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/5-1309\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,12,5]],"date-time":"2018-12-05T13:01:52Z","timestamp":1544014912000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/5-1309\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,6,9]]},"references-count":12,"URL":"https:\/\/doi.org\/10.12688\/f1000research.8964.1","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.9644.r14285","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.9644.r14282","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.9644.r14283","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.9644.r14282","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.9644.r14283","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.9644.r14285","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,6,9]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/5-1309\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.9644.r14285, Olivier Namy, Pierre Bertin, Institute for Integrative Biology of the Cell (I2BC), University of Paris-Sud, Orsay, France, 20 Jun 2016, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/5-1309\/v1#referee-response-14285","order":0,"name":"referee-response-14285","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.9644.r14282, Audrey M Michel, School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland, 21 Jun 2016, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/5-1309\/v1#referee-response-14282","order":1,"name":"referee-response-14282","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.9644.r14283, Ghislain Bidaut, Integrative Bioinformatics, Inserm, Aix-Marseille Universit\u00e9, CNRS and Institut Paoli-Calmettes, Centre de Recherche en Canc\u00e9rologie de Marseille, Marseille, France, 05 Jul 2016, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/5-1309\/v1#referee-response-14283","order":2,"name":"referee-response-14283","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was developed by the Functional Genomics Platform at Nice Sophia Antipolis, a partner of the National Infrastructure France G\u00e9nomique (ANR-10-INBS-09-03 and ANR-10-INBS-09-02) and PB\u2019s group, thanks to supports by the Canc\u00e9rop\u00f4le PACA and Commissariat aux Grands Investissements. RW was supported by Fondation ARC pour la recherche sur le cancer (SFI20121205973), and PB by ANR (ANR-12-BSVI-0023-02), Fondation pour la Recherche M\u00e9dicale (DEQ20130326464) and labex Signalife (ANR-11-LABX-0028-01). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}