{"id":"https://openalex.org/W2122532582","doi":"https://doi.org/10.1093/bioinformatics/btt085","title":"Nozzle: a report generation toolkit for data analysis pipelines","display_name":"Nozzle: a report generation toolkit for data analysis pipelines","publication_year":2013,"publication_date":"2013-02-17","ids":{"openalex":"https://openalex.org/W2122532582","doi":"https://doi.org/10.1093/bioinformatics/btt085","mag":"2122532582","pmid":"https://pubmed.ncbi.nlm.nih.gov/23419376"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt085","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt085","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/1089/48899147/bioinformatics_29_8_1089.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/29/8/1089/48899147/bioinformatics_29_8_1089.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066335313","display_name":"Nils Gehlenborg","orcid":"https://orcid.org/0000-0003-0327-8297"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nils Gehlenborg","raw_affiliation_strings":["1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA","institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076052555","display_name":"Michael S. Noble","orcid":"https://orcid.org/0000-0002-6704-1793"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael S. Noble","raw_affiliation_strings":["1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA","institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001392592","display_name":"Gad Getz","orcid":"https://orcid.org/0000-0002-0936-0753"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gad Getz","raw_affiliation_strings":["1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA","institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104109623","display_name":"Lynda Chin","orcid":null},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lynda Chin","raw_affiliation_strings":["1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA","institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022028438","display_name":"Peter J. Park","orcid":"https://orcid.org/0000-0001-9378-960X"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter J. Park","raw_affiliation_strings":["1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA","institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5022028438"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.559,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.89586697,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"29","issue":"8","first_page":"1089","last_page":"1091"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.16940000653266907,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.16940000653266907,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T11986","display_name":"Scientific Computing and Data Management","score":0.1445000022649765,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T13398","display_name":"Data Analysis with R","score":0.1315000057220459,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/pipeline-transport","display_name":"Pipeline transport","score":0.6175894141197205},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5937111973762512},{"id":"https://openalex.org/keywords/nozzle","display_name":"Nozzle","score":0.5879860520362854},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.43362075090408325},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2501639127731323},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1801145374774933},{"id":"https://openalex.org/keywords/aerospace-engineering","display_name":"Aerospace engineering","score":0.13260293006896973},{"id":"https://openalex.org/keywords/mechanical-engineering","display_name":"Mechanical engineering","score":0.11052632331848145}],"concepts":[{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.6175894141197205},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5937111973762512},{"id":"https://openalex.org/C56200935","wikidata":"https://www.wikidata.org/wiki/Q250840","display_name":"Nozzle","level":2,"score":0.5879860520362854},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.43362075090408325},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2501639127731323},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1801145374774933},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.13260293006896973},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.11052632331848145}],"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":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":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt085","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt085","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/1089/48899147/bioinformatics_29_8_1089.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:23419376","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23419376","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2965023","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3624805","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt085","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt085","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/1089/48899147/bioinformatics_29_8_1089.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":[{"display_name":"Industry, innovation and infrastructure","score":0.5699999928474426,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2664783788","display_name":null,"funder_award_id":"U24CA143845","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2857508635","display_name":null,"funder_award_id":"U24 CA143867","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320314070","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2122532582.pdf","grobid_xml":"https://content.openalex.org/works/W2122532582.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1520411860","https://openalex.org/W1977859620","https://openalex.org/W2002134496","https://openalex.org/W2136482257","https://openalex.org/W2137653635","https://openalex.org/W2157852151","https://openalex.org/W6631153645"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2360206036","https://openalex.org/W2086347189","https://openalex.org/W2377901036","https://openalex.org/W4327773545","https://openalex.org/W2884606178","https://openalex.org/W3179160715","https://openalex.org/W761656675","https://openalex.org/W3011610445","https://openalex.org/W2804496044"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"have":[2],"developed":[3],"Nozzle,":[4],"an":[5,10],"R":[6,65],"package":[7,49,66],"that":[8],"provides":[9],"Application":[11],"Programming":[12],"Interface":[13],"to":[14,26,53,60],"generate":[15],"HTML":[16],"reports":[17,58],"with":[18],"dynamic":[19],"user":[20],"interface":[21],"elements.":[22],"Nozzle":[23],"was":[24],"designed":[25],"facilitate":[27],"summarization":[28],"and":[29,74],"rapid":[30],"browsing":[31],"of":[32],"complex":[33],"results":[34],"in":[35],"data":[36,92],"analysis":[37],"pipelines":[38],"where":[39,56],"multiple":[40],"analyses":[41],"are":[42,77,93],"performed":[43],"frequently":[44],"on":[45,69],"big":[46],"datasets.":[47],"The":[48,64,81],"can":[50],"be":[51,61],"applied":[52],"any":[54],"project":[55],"user-friendly":[57],"need":[59],"created.":[62],"AVAILABILITY:":[63],"is":[67,84],"available":[68,78,86,94],"CRAN":[70],"at":[71,79,87,95],"http://cran.r-project.org/package=Nozzle.R1.":[72],"Examples":[73],"additional":[75],"materials":[76],"http://gdac.broadinstitute.org/nozzle.":[80],"source":[82],"code":[83],"also":[85],"http://www.github.com/parklab/Nozzle.":[88],"SUPPLEMENTARY":[89],"INFORMATION:":[90],"Supplementary":[91],"Bioinformatics":[96],"online.":[97]},"counts_by_year":[{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
