{"id":"https://openalex.org/W2129455748","doi":"https://doi.org/10.1186/1471-2105-15-s1-s11","title":"The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again","display_name":"The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2129455748","doi":"https://doi.org/10.1186/1471-2105-15-s1-s11","mag":"2129455748","pmid":"https://pubmed.ncbi.nlm.nih.gov/24564732"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-s1-s11","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s1-s11","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S1-S11","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/10.1186/1471-2105-15-S1-S11","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086246448","display_name":"Alejandra Gonz\u00e1lez-Beltr\u00e1n","orcid":"https://orcid.org/0000-0003-3499-8262"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Alejandra Gonz\u00e1lez-Beltr\u00e1n","raw_affiliation_strings":["Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK","Oxford e-Research Centre, University of Oxford,Oxford,UK"],"affiliations":[{"raw_affiliation_string":"Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Oxford e-Research Centre, University of Oxford,Oxford,UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038786156","display_name":"Steffen Neumann","orcid":"https://orcid.org/0000-0002-7899-7192"},"institutions":[{"id":"https://openalex.org/I315704651","display_name":"Leibniz Association","ror":"https://ror.org/01n6r0e97","country_code":"DE","type":"funder","lineage":["https://openalex.org/I315704651"]},{"id":"https://openalex.org/I4210110463","display_name":"Leibniz Institute of Plant Biochemistry","ror":"https://ror.org/01mzk5576","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210110463"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Steffen Neumann","raw_affiliation_strings":["Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Halle, 06120, Germany","Leibniz Institute of Plant Biochemistry Department of Stress and Developmental Biology Halle Germany"],"affiliations":[{"raw_affiliation_string":"Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Halle, 06120, Germany","institution_ids":["https://openalex.org/I4210110463"]},{"raw_affiliation_string":"Leibniz Institute of Plant Biochemistry Department of Stress and Developmental Biology Halle Germany","institution_ids":["https://openalex.org/I315704651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075052652","display_name":"Eamonn Maguire","orcid":"https://orcid.org/0000-0002-7277-7834"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Eamonn Maguire","raw_affiliation_strings":["Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK","Oxford e-Research Centre, University of Oxford,Oxford,UK"],"affiliations":[{"raw_affiliation_string":"Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Oxford e-Research Centre, University of Oxford,Oxford,UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008806860","display_name":"Susanna\u2010Assunta Sansone","orcid":"https://orcid.org/0000-0001-5306-5690"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Susanna-Assunta Sansone","raw_affiliation_strings":["Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK","Oxford e-Research Centre, University of Oxford,Oxford,UK"],"affiliations":[{"raw_affiliation_string":"Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Oxford e-Research Centre, University of Oxford,Oxford,UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018395535","display_name":"Philippe Rocca\u2010Serra","orcid":"https://orcid.org/0000-0001-9853-5668"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Philippe Rocca-Serra","raw_affiliation_strings":["Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK","Oxford e-Research Centre, University of Oxford,Oxford,UK"],"affiliations":[{"raw_affiliation_string":"Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Oxford e-Research Centre, University of Oxford,Oxford,UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5086246448"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.8503,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.85524111,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"15","issue":"S1","first_page":"S11","last_page":"S11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9958000183105469,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9958000183105469,"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":0.9904000163078308,"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/T11937","display_name":"Research Data Management Practices","score":0.9866999983787537,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.9456303119659424},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.8136086463928223},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7692466974258423},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.5876801609992981},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5182650089263916},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.49825263023376465},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40860649943351746},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3882206678390503},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.273916631937027},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1405123770236969},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1297052502632141}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9456303119659424},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.8136086463928223},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7692466974258423},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.5876801609992981},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5182650089263916},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.49825263023376465},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40860649943351746},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3882206678390503},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.273916631937027},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1405123770236969},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1297052502632141},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-15-s1-s11","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s1-s11","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S1-S11","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:24564732","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24564732","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:europepmc.org:3005796","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4015122","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:10.1186/1471-2105-15-s1-s11","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s1-s11","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S1-S11","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":0.5099999904632568,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G3339699563","display_name":null,"funder_award_id":"BB/J020265/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G412979241","display_name":null,"funder_award_id":"BB/I000771/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G651559499","display_name":null,"funder_award_id":"BB/I025840/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7775520706","display_name":null,"funder_award_id":"BB/E025080/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8455383874","display_name":null,"funder_award_id":"BB/I02612X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320309622","display_name":"Harvard University","ror":"https://ror.org/03vek6s52"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2129455748.pdf","grobid_xml":"https://content.openalex.org/works/W2129455748.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W143096088","https://openalex.org/W1544923801","https://openalex.org/W1964010911","https://openalex.org/W1969165973","https://openalex.org/W2069928158","https://openalex.org/W2090167567","https://openalex.org/W2094953050","https://openalex.org/W2110017950","https://openalex.org/W2113153354","https://openalex.org/W2116634113","https://openalex.org/W2118258530","https://openalex.org/W2120358246","https://openalex.org/W2123152121","https://openalex.org/W2129687578","https://openalex.org/W2130430745","https://openalex.org/W2130542009","https://openalex.org/W2132239943","https://openalex.org/W2138598227","https://openalex.org/W2139252617","https://openalex.org/W2139846209","https://openalex.org/W2140665097","https://openalex.org/W2141297584","https://openalex.org/W2144303444","https://openalex.org/W2149378423","https://openalex.org/W2152239989","https://openalex.org/W2157918066","https://openalex.org/W2159702756","https://openalex.org/W2160697532","https://openalex.org/W2327661356","https://openalex.org/W4253880235"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2011682793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W4223449272","https://openalex.org/W2978247079","https://openalex.org/W43224192","https://openalex.org/W90653389","https://openalex.org/W3046984657","https://openalex.org/W2053943328"],"abstract_inverted_index":{"The":[0,23],"Risa":[1],"package":[2],"is":[3,29],"available":[4],"since":[5],"Bioconductor":[6,15,35],"2.11":[7],"(version":[8],"1.0.0)":[9],"and":[10,21,36],"version":[11,25],"1.2.1":[12],"appeared":[13],"in":[14,34],"2.12,":[16],"both":[17],"along":[18],"with":[19],"documentation":[20],"examples.":[22],"latest":[24],"of":[26],"the":[27,31,45],"code":[28],"at":[30],"development":[32],"branch":[33],"can":[37],"also":[38],"be":[39],"accessed":[40],"from":[41],"GitHub":[42],"https://github.com/ISA-tools/Risa,":[43],"where":[44],"issue":[46],"tracker":[47],"allows":[48],"users":[49],"to":[50],"report":[51],"bugs":[52],"or":[53],"feature":[54],"requests.":[55]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
