{"id":"https://openalex.org/W2137705643","doi":"https://doi.org/10.1186/s12859-015-0729-3","title":"htsint: a Python library for sequencing pipelines that combines data through gene set generation","display_name":"htsint: a Python library for sequencing pipelines that combines data through gene set generation","publication_year":2015,"publication_date":"2015-09-24","ids":{"openalex":"https://openalex.org/W2137705643","doi":"https://doi.org/10.1186/s12859-015-0729-3","mag":"2137705643","pmid":"https://pubmed.ncbi.nlm.nih.gov/26399714"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0729-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0729-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0729-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0729-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062019583","display_name":"Adam Richards","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Adam J. Richards","raw_affiliation_strings":["Station d'Ecologie Exp\u00e9rimentale du CNRS, USR 2936, Route du CNRS, Moulis, 09200, France. adamricha@gmail.com","Station d\u2019Ecologie Experimentale du CNRS, Moulis, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Station d'Ecologie Exp\u00e9rimentale du CNRS, USR 2936, Route du CNRS, Moulis, 09200, France. adamricha@gmail.com","institution_ids":[]},{"raw_affiliation_string":"Station d\u2019Ecologie Experimentale du CNRS, Moulis, France","institution_ids":["https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076510192","display_name":"Anthony Herrel","orcid":"https://orcid.org/0000-0003-0991-4434"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE","FR"],"is_corresponding":false,"raw_author_name":"Anthony Herrel","raw_affiliation_strings":["Ghent University, Evolutionary Morphology of Vertebrates, K.L. Ledeganckstraat 35, Ghent, B-9000, Belgium. anthony.herrel@mnhn.fr","UMR 7179 CNRS/MNHN, D\u00e9partement d'Ecologie et de Gestion de la Biodiversit\u00e9 57 rue Cuvier, Case postale 55, Paris, 75231, France. anthony.herrel@mnhn.fr","UMR 7179 CNRS/MNHN, D\u00e9partement d\u2019Ecologie et de Gestion de la Biodiversit\u00e9 57 rue Cuvier, Paris, France","Ghent University, Evolutionary Morphology of Vertebrates, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ghent University, Evolutionary Morphology of Vertebrates, K.L. Ledeganckstraat 35, Ghent, B-9000, Belgium. anthony.herrel@mnhn.fr","institution_ids":[]},{"raw_affiliation_string":"UMR 7179 CNRS/MNHN, D\u00e9partement d'Ecologie et de Gestion de la Biodiversit\u00e9 57 rue Cuvier, Case postale 55, Paris, 75231, France. anthony.herrel@mnhn.fr","institution_ids":[]},{"raw_affiliation_string":"UMR 7179 CNRS/MNHN, D\u00e9partement d\u2019Ecologie et de Gestion de la Biodiversit\u00e9 57 rue Cuvier, Paris, France","institution_ids":["https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Ghent University, Evolutionary Morphology of Vertebrates, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030755565","display_name":"Camille Bonneaud","orcid":"https://orcid.org/0000-0003-2248-3288"},"institutions":[{"id":"https://openalex.org/I4210162824","display_name":"Station d\u2019\u00c9cologie Th\u00e9orique et Exp\u00e9rimentale","ror":"https://ror.org/05d6wfd23","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I134560555","https://openalex.org/I4210107625","https://openalex.org/I4210123595","https://openalex.org/I4210162824","https://openalex.org/I4412460029"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"Camille Bonneaud","raw_affiliation_strings":["Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn TR10 9FE, Cornwall, UK. C.Bonneaud@exeter.ac.uk","Station d'Ecologie Exp\u00e9rimentale du CNRS, USR 2936, Route du CNRS, Moulis, 09200, France. C.Bonneaud@exeter.ac.uk","Station d\u2019Ecologie Exp\u00e9rimentale du CNRS, Moulis, France","Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn TR10 9FE, Cornwall, UK. C.Bonneaud@exeter.ac.uk","institution_ids":[]},{"raw_affiliation_string":"Station d'Ecologie Exp\u00e9rimentale du CNRS, USR 2936, Route du CNRS, Moulis, 09200, France. C.Bonneaud@exeter.ac.uk","institution_ids":[]},{"raw_affiliation_string":"Station d\u2019Ecologie Exp\u00e9rimentale du CNRS, Moulis, France","institution_ids":["https://openalex.org/I4210162824","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, UK","institution_ids":["https://openalex.org/I23923803"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5062019583"],"corresponding_institution_ids":["https://openalex.org/I1294671590"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1506,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56923009,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"16","issue":"1","first_page":"307","last_page":"307"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5623000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5623000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.19419999420642853,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0763000026345253,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6167764663696289},{"id":"https://openalex.org/keywords/ensembl","display_name":"Ensembl","score":0.577656626701355},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5534906387329102},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.5383307933807373},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.515496551990509},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.49268394708633423},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4822433888912201},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.48095598816871643},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4421238899230957},{"id":"https://openalex.org/keywords/gene-nomenclature","display_name":"Gene nomenclature","score":0.41831257939338684},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4177137613296509},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35681581497192383},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3002975285053253},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10226336121559143}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6167764663696289},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.577656626701355},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5534906387329102},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.5383307933807373},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.515496551990509},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.49268394708633423},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4822433888912201},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.48095598816871643},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4421238899230957},{"id":"https://openalex.org/C62177273","wikidata":"https://www.wikidata.org/wiki/Q5531556","display_name":"Gene nomenclature","level":4,"score":0.41831257939338684},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4177137613296509},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35681581497192383},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3002975285053253},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10226336121559143},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.0},{"id":"https://openalex.org/C514705636","wikidata":"https://www.wikidata.org/wiki/Q863247","display_name":"Nomenclature","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-015-0729-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0729-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0729-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26399714","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26399714","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:hal-02145303v1","is_oa":false,"landing_page_url":"https://hal.science/hal-02145303","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2015, 16 (1), &#x27E8;10.1186/s12859-015-0729-3&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:archive.ugent.be:7165038","is_oa":true,"landing_page_url":"http://hdl.handle.net/1854/LU-7165038","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:europepmc.org:3554422","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4581156","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0729-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0729-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0729-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2151424815","display_name":null,"funder_award_id":"NE/M00256X","funder_id":"https://openalex.org/F4320334631","funder_display_name":"Natural Environment Research Council"},{"id":"https://openalex.org/G4748312811","display_name":null,"funder_award_id":"ANR- 09-PEXT-003","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G584690411","display_name":"Evolution of phenotypic plasticity in an emerging pathogen","funder_award_id":"NE/M00256X/1","funder_id":"https://openalex.org/F4320334631","funder_display_name":"Natural Environment Research Council"},{"id":"https://openalex.org/G5936007187","display_name":null,"funder_award_id":"ANR-09-PEXT-003","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7084180774","display_name":null,"funder_award_id":"NE/M00256X/1","funder_id":"https://openalex.org/F4320320022","funder_display_name":"Sight Research UK"},{"id":"https://openalex.org/G7093479516","display_name":null,"funder_award_id":"09-PEXT-003","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7872016925","display_name":null,"funder_award_id":"NE/M00256X/1","funder_id":"https://openalex.org/F4320334631","funder_display_name":"Natural Environment Research Council"}],"funders":[{"id":"https://openalex.org/F4320320022","display_name":"Sight Research UK","ror":"https://ror.org/03z2py885"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320334631","display_name":"Natural Environment Research Council","ror":"https://ror.org/02b5d8509"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2137705643.pdf","grobid_xml":"https://content.openalex.org/works/W2137705643.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1647729745","https://openalex.org/W1975588116","https://openalex.org/W1981276685","https://openalex.org/W1981509058","https://openalex.org/W2004351228","https://openalex.org/W2011301426","https://openalex.org/W2020859582","https://openalex.org/W2027895157","https://openalex.org/W2057119643","https://openalex.org/W2059224185","https://openalex.org/W2079324889","https://openalex.org/W2084168100","https://openalex.org/W2101536220","https://openalex.org/W2103017472","https://openalex.org/W2113930937","https://openalex.org/W2114850508","https://openalex.org/W2117805756","https://openalex.org/W2126045294","https://openalex.org/W2126449841","https://openalex.org/W2130410032","https://openalex.org/W2131071295","https://openalex.org/W2132022337","https://openalex.org/W2134526812","https://openalex.org/W2134736660","https://openalex.org/W2135230352","https://openalex.org/W2142678478","https://openalex.org/W2158050409","https://openalex.org/W2158217645","https://openalex.org/W2159675211","https://openalex.org/W2160697532","https://openalex.org/W2165674132","https://openalex.org/W2165874743","https://openalex.org/W2166550754","https://openalex.org/W2166890927","https://openalex.org/W2169528473","https://openalex.org/W2605068739","https://openalex.org/W2912485311","https://openalex.org/W2999905431","https://openalex.org/W4285719527","https://openalex.org/W6665394523","https://openalex.org/W6675471023"],"related_works":["https://openalex.org/W3111061871","https://openalex.org/W2146014453","https://openalex.org/W2464717012","https://openalex.org/W4230762195","https://openalex.org/W2042690128","https://openalex.org/W3118378687","https://openalex.org/W2965072475","https://openalex.org/W2183351625","https://openalex.org/W2952377671","https://openalex.org/W4386011922"],"abstract_inverted_index":{"BACKGROUND:":[0],"Sequencing":[1],"technologies":[2],"provide":[3],"a":[4,33,61,77,130,153,159,171,177,203,249],"wealth":[5],"of":[6,10,35,80,108,156,168,173,180,202,205,230,241],"details":[7],"in":[8,120,129,224,238],"terms":[9,44],"genes,":[11,142,157],"expression,":[12,184],"splice":[13],"variants,":[14],"polymorphisms,":[15],"and":[16,52,69,176,212],"other":[17,239],"features.":[18],"A":[19],"standard":[20],"for":[21,195],"sequencing":[22,222],"analysis":[23],"pipelines":[24,223],"is":[25,110,136,245],"to":[26,64,97,111,122,139,165,215,234],"put":[27],"genomic":[28],"or":[29,117,197],"transcriptomic":[30,181],"features":[31,182],"into":[32],"context":[34],"known":[36,78],"functional":[37,124,145,217],"information,":[38],"but":[39,226],"the":[40,57,87,98,141,163,186,227],"relationships":[41],"between":[42,74],"ontology":[43],"are":[45],"often":[46],"ignored.":[47],"For":[48],"RNA-Seq,":[49],"considering":[50],"genes":[51,128],"their":[53],"genetic":[54],"variants":[55],"at":[56,254],"group":[58],"level":[59,82],"enables":[60],"convenient":[62],"way":[63,164],"both":[65],"integrate":[66],"annotation":[67,113],"data":[68,90],"detect":[70],"small":[71],"coordinated":[72],"changes":[73],"experimental":[75],"conditions,":[76],"caveat":[79],"gene":[81,101,132,148,174,187],"analyses.":[83],"RESULTS:":[84],"We":[85],"introduce":[86],"high":[88],"throughput":[89],"integration":[91],"tool,":[92],"htsint,":[93],"as":[94,248],"an":[95,166],"extension":[96],"commonly":[99,206],"used":[100,138,237],"set":[102],"enrichment":[103],"frameworks.":[104],"The":[105,147,210,243],"central":[106],"aim":[107],"htsint":[109,191,231],"compile":[112],"information":[114],"from":[115,152],"one":[116,201],"more":[118],"taxa":[119],"order":[121],"calculate":[123],"distances":[125],"among":[126],"all":[127,162],"specified":[131],"space.":[133],"Spectral":[134],"clustering":[135],"then":[137],"partition":[140],"thereby":[143],"generating":[144],"modules.":[146],"space":[149],"can":[150,192],"range":[151],"targeted":[154],"list":[155],"like":[158],"specific":[160],"pathway,":[161],"ensemble":[167],"genomes.":[169],"Given":[170],"collection":[172],"sets":[175,188],"count":[178],"matrix":[179],"(e.g.":[183],"polymorphisms),":[185],"produced":[189],"by":[190],"be":[193,236],"tested":[194],"'enrichment'":[196],"conditional":[198],"differences":[199],"using":[200],"number":[204],"available":[207,247],"packages.":[208],"CONCLUSION:":[209],"database":[211],"bundled":[213],"tools":[214],"generate":[216],"modules":[218],"were":[219],"designed":[220],"with":[221],"mind,":[225],"toolkit":[228],"nature":[229],"allows":[232],"it":[233],"also":[235],"areas":[240],"genomics.":[242],"software":[244],"freely":[246],"Python":[250],"library":[251],"through":[252],"GitHub":[253],"https://github.com/ajrichards/htsint.":[255]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
