{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T10:15:52Z","timestamp":1772878552380,"version":"3.50.1"},"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":2080,"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":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput screens (HTS) by RNAi or small molecules are among the most promising tools in functional genomics. They enable researchers to observe detailed reactions to experimental perturbations on a genome-wide scale. While there is a core set of computational approaches used in many publications to analyze these data, a specialized software combining them and making them easily accessible has so far been missing.<\/jats:p>\n               <jats:p>Results: Here we describe HTSanalyzeR, a flexible software to build integrated analysis pipelines for HTS data that contains over-representation analysis, gene set enrichment analysis, comparative gene set analysis and rich sub-network identification. HTSanalyzeR interfaces with commonly used pre-processing packages for HTS data and presents its results as HTML pages and network plots.<\/jats:p>\n               <jats:p>Availability: Our software is written in the R language and freely available via the Bioconductor project at http:\/\/www.bioconductor.org.<\/jats:p>\n               <jats:p>Contact: \u00a0florian.markowetz@cancer.org.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr028","type":"journal-article","created":{"date-parts":[[2011,1,23]],"date-time":"2011-01-23T01:16:30Z","timestamp":1295745390000},"page":"879-880","source":"Crossref","is-referenced-by-count":120,"title":["HTSanalyzeR: an R\/Bioconductor package for integrated network analysis of high-throughput screens"],"prefix":"10.1093","volume":"27","author":[{"given":"Xin","family":"Wang","sequence":"first","affiliation":[{"name":"1 Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, 2Department of Oncology, University of Cambridge and 3Cambridge Computational Biology Institute and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK"},{"name":"1 Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, 2Department of Oncology, University of Cambridge and 3Cambridge Computational Biology Institute and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camille","family":"Terfve","sequence":"additional","affiliation":[{"name":"1 Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, 2Department of Oncology, University of Cambridge and 3Cambridge Computational Biology Institute and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John C.","family":"Rose","sequence":"additional","affiliation":[{"name":"1 Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, 2Department of Oncology, University of Cambridge and 3Cambridge Computational Biology Institute and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian","family":"Markowetz","sequence":"additional","affiliation":[{"name":"1 Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, 2Department of Oncology, University of Cambridge and 3Cambridge Computational Biology Institute and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK"},{"name":"1 Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, 2Department of Oncology, University of Cambridge and 3Cambridge Computational Biology Institute and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,1,22]]},"reference":[{"key":"2023012511553806200_B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. the gene ontology consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. 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