{"id":"https://openalex.org/W2108274758","doi":"https://doi.org/10.1093/bioinformatics/btp169","title":"Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x","display_name":"Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x","publication_year":2009,"publication_date":"2009-04-05","ids":{"openalex":"https://openalex.org/W2108274758","doi":"https://doi.org/10.1093/bioinformatics/btp169","mag":"2108274758","pmid":"https://pubmed.ncbi.nlm.nih.gov/19349284"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp169","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp169","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/11/1447/945602/btp169.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/11/1447/945602/btp169.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081015175","display_name":"Vincent J. Carey","orcid":"https://orcid.org/0000-0003-4046-0063"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vincent J. Carey","raw_affiliation_strings":["1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019971412","display_name":"Adam R. Davis","orcid":"https://orcid.org/0000-0002-7949-4116"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam R. Davis","raw_affiliation_strings":["1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101458328","display_name":"Michael Lawrence","orcid":null},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael F. Lawrence","raw_affiliation_strings":["1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039040940","display_name":"Robert Gentleman","orcid":"https://orcid.org/0000-0003-4505-9893"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Gentleman","raw_affiliation_strings":["1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054459458","display_name":"Benjamin A. Raby","orcid":"https://orcid.org/0000-0003-2206-5748"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin A. Raby","raw_affiliation_strings":["1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA","institution_ids":["https://openalex.org/I4210089486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5477,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.67472038,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"25","issue":"11","first_page":"1447","last_page":"1448"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9243999719619751,"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":0.9243999719619751,"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":0.010200000368058681,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.007600000128149986,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/bioconductor","display_name":"Bioconductor","score":0.9877040386199951},{"id":"https://openalex.org/keywords/international-hapmap-project","display_name":"International HapMap Project","score":0.8624898195266724},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5366209745407104},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.50468909740448},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5040551424026489},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.49746015667915344},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.40426719188690186},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3585239052772522},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.35350751876831055},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34534281492233276},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28700631856918335},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.27950555086135864}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9877040386199951},{"id":"https://openalex.org/C177580304","wikidata":"https://www.wikidata.org/wiki/Q1147298","display_name":"International HapMap Project","level":5,"score":0.8624898195266724},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5366209745407104},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.50468909740448},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5040551424026489},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.49746015667915344},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.40426719188690186},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3585239052772522},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.35350751876831055},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34534281492233276},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28700631856918335},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.27950555086135864}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp169","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp169","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/11/1447/945602/btp169.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19349284","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19349284","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2682516","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2682516","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp169","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp169","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/11/1447/945602/btp169.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5899999737739563,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G3957019476","display_name":null,"funder_award_id":"R01 HL086601","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108274758.pdf","grobid_xml":"https://content.openalex.org/works/W2108274758.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1993507775","https://openalex.org/W2043842514","https://openalex.org/W2060181803","https://openalex.org/W2107300110","https://openalex.org/W2112087830","https://openalex.org/W2145090915","https://openalex.org/W2154998360","https://openalex.org/W6665590536"],"related_works":["https://openalex.org/W1017625355","https://openalex.org/W3032744250","https://openalex.org/W1593502352","https://openalex.org/W2108274758","https://openalex.org/W1514925303","https://openalex.org/W1663907732","https://openalex.org/W2111793653","https://openalex.org/W2142923264","https://openalex.org/W2356514887","https://openalex.org/W2125327003"],"abstract_inverted_index":{"SUMMARY:":[0],"Associations":[1],"between":[2],"DNA":[3],"polymorphisms":[4],"and":[5,15,19,35,44,49,59,73],"mRNA":[6],"abundance":[7],"are":[8],"a":[9],"natural":[10],"target":[11],"of":[12,22,42,47],"genetic":[13],"investigations,":[14],"microarrays":[16],"facilitate":[17],"genome-wide":[18],"transcriptome-wide":[20],"surveys":[21],"these":[23],"associations.":[24],"This":[25],"work":[26],"is":[27],"motivated":[28],"by":[29],"emerging":[30],"requirements":[31],"for":[32],"data":[33],"architectures":[34],"algorithm":[36],"interfaces":[37],"to":[38],"allow":[39],"flexible":[40],"exploration":[41],"public":[43],"private":[45],"archives":[46],"genotyping":[48],"expression":[50,62],"arrays.":[51],"Using":[52],"R/Bioconductor":[53],"facilities,":[54],"Phase":[55],"II":[56],"HapMap":[57],"genotypes":[58],"Illumina":[60],"47K":[61],"assay":[63],"results":[64],"archived":[65],"on":[66,92],"multiple":[67],"populations":[68],"may":[69],"be":[70],"interactively":[71],"explored":[72],"analyzed":[74],"using":[75],"commodity":[76],"hardware.":[77],"AVAILABILITY":[78],"AND":[79],"IMPLEMENTATION:":[80],"Open":[81],"Source.":[82],"Bioconductor":[83],"2.3":[84],"packages":[85],"GGtools,":[86],"GGBase,":[87],"GGdata,":[88],"hmyriB36.":[89],"Freely":[90],"available":[91],"the":[93],"web":[94],"at":[95],"(http://www.bioconductor.org).":[96]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}