{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T20:10:02Z","timestamp":1748635802305,"version":"3.41.0"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,9,24]],"date-time":"2015-09-24T00:00:00Z","timestamp":1443052800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche (FR)","doi-asserted-by":"publisher","award":["ANR- 09-PEXT-003"],"award-info":[{"award-number":["ANR- 09-PEXT-003"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-015-0729-3","type":"journal-article","created":{"date-parts":[[2015,9,24]],"date-time":"2015-09-24T01:18:34Z","timestamp":1443057514000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["htsint: a Python library for sequencing pipelines that combines data through gene set generation"],"prefix":"10.1186","volume":"16","author":[{"given":"Adam J.","family":"Richards","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Herrel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camille","family":"Bonneaud","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,9,24]]},"reference":[{"issue":"1","key":"729_CR1","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nrg2484","volume":"10","author":"Z Wang","year":"2009","unstructured":"Wang Z, Gerstein M, Snyder M. RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet. 2009; 10(1):57\u201363.","journal-title":"Nat Rev Genet"},{"issue":"9","key":"729_CR2","doi-asserted-by":"publisher","first-page":"2981","DOI":"10.1073\/pnas.0308661100","volume":"101","author":"A Tanay","year":"2004","unstructured":"Tanay A, Sharan R, Kupiec M, Shamir R. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. PNAS. 2004; 101(9):2981\u2013986.","journal-title":"PNAS"},{"issue":"43","key":"729_CR3","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al.Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. PNAS. 2005; 102(43):15545\u201350.","journal-title":"PNAS"},{"issue":"18","key":"729_CR4","doi-asserted-by":"publisher","first-page":"3587","DOI":"10.1093\/bioinformatics\/bti565","volume":"21","author":"P Khatri","year":"2005","unstructured":"Khatri P, Dr\u0103ghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics. 2005; 21(18):3587\u2013595.","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"729_CR5","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1093\/nar\/gkj102","volume":"34","author":"M Kanehisa","year":"2006","unstructured":"Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, et al.From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006; 34(Database issue):354\u20137.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"729_CR6","first-page":"25","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al.Gene ontology: tool for the unification of biology. Nat Geosci. 2000; 25(1):25\u20139.","journal-title":"Nat Geosci"},{"issue":"8","key":"729_CR7","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1093\/bioinformatics\/btm051","volume":"23","author":"JJ Goeman","year":"2007","unstructured":"Goeman JJ, B\u00fchlmann P. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics. 2007; 23(8):980\u20137.","journal-title":"Bioinformatics"},{"issue":"3","key":"729_CR8","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1093\/bib\/bbr049","volume":"13","author":"JH Hung","year":"2012","unstructured":"Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C. Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform. 2012; 13(3):281\u201391.","journal-title":"Brief Bioinform"},{"issue":"4","key":"729_CR9","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1093\/bib\/bbt002","volume":"15","author":"H Maciejewski","year":"2013","unstructured":"Maciejewski H. Gene set analysis methods: statistical models and methodological differences. Brief Bioinform. 2013; 15(4):504\u201318.","journal-title":"Brief Bioinform"},{"issue":"1","key":"729_CR10","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1186\/s12859-014-0397-8","volume":"15","author":"Y Rahmatallah","year":"2014","unstructured":"Rahmatallah Y, Emmert-Streib F, Glazko G. Comparative evaluation of gene set analysis approaches for RNA-Seq data. BMC Bioinforma. 2014; 15(1):397.","journal-title":"BMC Bioinforma"},{"issue":"1","key":"729_CR11","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"DW Huang","year":"2009","unstructured":"Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44\u201357.","journal-title":"Nat Protoc"},{"issue":"3","key":"729_CR12","doi-asserted-by":"publisher","first-page":"1000703","DOI":"10.1371\/journal.pcbi.1000703","volume":"6","author":"G Fang","year":"2010","unstructured":"Fang G, Bhardwaj N, Robilotto R, Gerstein MB. Getting started in gene orthology and functional analysis. PLoS Comput Biol. 2010; 6(3):1000703.","journal-title":"PLoS Comput Biol"},{"issue":"11","key":"729_CR13","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1371\/journal.pcbi.0030199","volume":"3","author":"S Bassi","year":"2007","unstructured":"Bassi S. A primer on python for life science researchers. PLoS Comput Biol. 2007; 3(11):199.","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"729_CR14","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","volume":"31","author":"S Anders","year":"2015","unstructured":"Anders S, Pyl PT, Huber W. HTSeq - A Python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31(2):166\u20139.","journal-title":"Bioinformatics"},{"key":"729_CR15","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology. 2004; 5:80.","journal-title":"Genome Biology"},{"issue":"12","key":"729_CR16","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1093\/bioinformatics\/btu090","volume":"30","author":"X Wang","year":"2014","unstructured":"Wang X, Cairns MJ. Seqgsea: a bioconductor package for gene set enrichment analysis of rna-seq data integrating differential expression and splicing. Bioinformatics. 2014; 30(12):1777\u20139.","journal-title":"Bioinformatics"},{"issue":"1","key":"729_CR17","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1214\/07-AOAS101","volume":"1","author":"B Efron","year":"2007","unstructured":"Efron B, Tibshirani R. On testing the significance of sets of genes. Ann Appl Stat. 2007; 1(1):107\u201329.","journal-title":"Ann Appl Stat"},{"issue":"Database issue","key":"729_CR18","first-page":"191","volume":"42","author":"U Consortium","year":"2014","unstructured":"Consortium U. Activities at the universal protein resource (uniprot). Nucleic Acids Res. 2014; 42(Database issue):191\u20138.","journal-title":"Nucleic Acids Res"},{"key":"729_CR19","doi-asserted-by":"crossref","unstructured":"Hagberg AA, Schult DA, Swart PJ. Exploring network structure, dynamics, and function using NetworkX In: Varoquaux G, Vaught T, Millman J, editors. Proceedings of the 7th Python in Science Conference (SciPy 2008). Pasadena, CA, USA: 2008. p. 11\u201316.","DOI":"10.25080\/TCWV9851"},{"issue":"3","key":"729_CR20","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1109\/MCSE.2007.55","volume":"9","author":"JD Hunter","year":"2007","unstructured":"Hunter JD. Matplotlib: A 2d graphics environment. Comput Sci Eng. 2007; 9(3):90\u20135.","journal-title":"Comput Sci Eng"},{"issue":"11","key":"729_CR21","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al.Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498\u2013504.","journal-title":"Genome Res"},{"key":"729_CR22","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al.BLAST+: architecture and applications. BMC Bioinforma. 2009; 10:421.","journal-title":"BMC Bioinforma"},{"issue":"11","key":"729_CR23","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","volume":"25","author":"PJA Cock","year":"2009","unstructured":"Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al.Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009; 25(11):1422\u20133.","journal-title":"Bioinformatics"},{"key":"729_CR24","volume-title":"Proceedings of IJCAI. IJCAI\u201995","author":"P Resnik","year":"1995","unstructured":"Resnik P. Using information content to evaluate semantic similarity in a taxonomy. In: Proceedings of IJCAI. IJCAI\u201995. San Francisco, CA, USA: Morgan Kaufmann Publishers Inc.: 1995. p. 448\u201353."},{"key":"729_CR25","volume-title":"Proceedings of the Fifteenth International Conference on Machine Learning. ICML \u201998","author":"D Lin","year":"1998","unstructured":"Lin D. An information-theoretic definition of similarity. In: Proceedings of the Fifteenth International Conference on Machine Learning. ICML \u201998. San Francisco, CA, USA: Morgan Kaufmann Publishers Inc.: 1998. p. 296\u2013304."},{"issue":"Suppl 3","key":"729_CR26","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1752-0509-6-S3-S7","volume":"6","author":"AJ Richards","year":"2012","unstructured":"Richards AJ, Schwacke JH, Rohrer B, Cowart LA, Lu X. Revealing functionally coherent subsets using a spectral clustering and an information integration approach. BMC Syst Biol. 2012; 6(Suppl 3):7.","journal-title":"BMC Syst Biol"},{"issue":"7","key":"729_CR27","doi-asserted-by":"publisher","first-page":"1000443","DOI":"10.1371\/journal.pcbi.1000443","volume":"5","author":"C Pesquita","year":"2009","unstructured":"Pesquita C, Faria D, Falc\u00e3o AO, Lord P, Couto FM. Semantic similarity in biomedical ontologies. PLoS Comput Biol. 2009; 5(7):1000443.","journal-title":"PLoS Comput Biol"},{"key":"729_CR28","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1007\/BF01386390","volume":"1","author":"EW Dijkstra","year":"1959","unstructured":"Dijkstra EW. A note on two problems in connexion with graphs. Numer Math. 1959; 1:269\u201371.","journal-title":"Numer Math"},{"key":"729_CR29","volume-title":"Advances in Neural Information Processing Systems 14","author":"AY Ng","year":"2001","unstructured":"Ng AY, Jordan MI, Weiss Y. On spectral clustering: Analysis and an algorithm In: Dietterich TG, Becker S, Ghahramani Z, editors. Advances in Neural Information Processing Systems 14. Cambridge, MA: MIT Press: 2001. p. 849\u201356."},{"issue":"5978","key":"729_CR30","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1126\/science.1183670","volume":"328","author":"U Hellsten","year":"2010","unstructured":"Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, et al.The genome of the western clawed frog Xenopus tropicalis. Science. 2010; 328(5978):633\u20136.","journal-title":"Science"},{"issue":"1","key":"729_CR31","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1101\/gr.141424.112","volume":"23","author":"MH Tan","year":"2013","unstructured":"Tan MH, Au KF, Yablonovitch AL, Wills AE, Chuang J, Baker JC, et al.RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res. 2013; 23(1):201\u201316.","journal-title":"Genome Res"},{"issue":"Database issue","key":"729_CR32","first-page":"761","volume":"36","author":"JB Bowes","year":"2008","unstructured":"Bowes JB, Snyder KA, Segerdell E, Gibb R, Jarabek C, Noumen E, et al.Xenbase: a xenopus biology and genomics resource. Nucleic Acids Res. 2008; 36(Database issue):761\u20137.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"729_CR33","doi-asserted-by":"publisher","first-page":"1002533","DOI":"10.1371\/journal.pcbi.1002533","volume":"8","author":"N Skunca","year":"2012","unstructured":"Skunca N, Altenhoff A, Dessimoz C. Quality of computationally inferred gene ontology annotations. PLoS Comput Biol. 2012; 8(5):1002533.","journal-title":"PLoS Comput Biol"},{"key":"729_CR34","doi-asserted-by":"crossref","unstructured":"Richards A, Kosinski A, Bonneaud C, Legrand D, Owzar K. lpEdit: an editor to facilitate reproducible analysis via literate programming In: van der Walt S, Millman J, Huff K, editors. Proceedings of the 12th Python in Science Conference: 2013. p. 85\u201389.","DOI":"10.25080\/Majora-8b375195-00e"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0729-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-015-0729-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0729-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T19:51:20Z","timestamp":1748634680000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-015-0729-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,9,24]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["729"],"URL":"https:\/\/doi.org\/10.1186\/s12859-015-0729-3","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2015,9,24]]},"article-number":"307"}}