{"id":"https://openalex.org/W2527533149","doi":"https://doi.org/10.1093/bioinformatics/btw624","title":"The START App: a web-based RNAseq analysis and visualization resource","display_name":"The START App: a web-based RNAseq analysis and visualization resource","publication_year":2016,"publication_date":"2016-09-29","ids":{"openalex":"https://openalex.org/W2527533149","doi":"https://doi.org/10.1093/bioinformatics/btw624","mag":"2527533149","pmid":"https://pubmed.ncbi.nlm.nih.gov/28171615"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw624","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw624","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/447/25416915/btw624.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/33/3/447/25416915/btw624.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031492756","display_name":"Jonathan W. Nelson","orcid":"https://orcid.org/0000-0003-1456-9399"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan W Nelson","raw_affiliation_strings":["The Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110862990","display_name":"Jiri Sklenar","orcid":null},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiri Sklenar","raw_affiliation_strings":["The Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028336744","display_name":"Anthony P. Barnes","orcid":"https://orcid.org/0000-0002-4598-9591"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anthony P Barnes","raw_affiliation_strings":["Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067245152","display_name":"Jessica Minnier","orcid":"https://orcid.org/0000-0002-3527-2757"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I25790992","display_name":"Cardiovascular Institute of the South","ror":"https://ror.org/02c2gwm94","country_code":"US","type":"other","lineage":["https://openalex.org/I25790992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jessica Minnier","raw_affiliation_strings":["School of Public Health, Oregon Health & Science University, Portland, OR, USA","The Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA","The Knight Cardiovascular Institute,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Public Health, Oregon Health & Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"The Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"The Knight Cardiovascular Institute,","institution_ids":["https://openalex.org/I25790992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067245152"],"corresponding_institution_ids":["https://openalex.org/I165690674","https://openalex.org/I25790992"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":6.3214,"has_fulltext":true,"cited_by_count":102,"citation_normalized_percentile":{"value":0.97020674,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"3","first_page":"447","last_page":"449"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.6158000230789185,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.6158000230789185,"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/T10885","display_name":"Gene expression and cancer classification","score":0.0877000018954277,"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":0.06759999692440033,"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/upload","display_name":"Upload","score":0.9336698651313782},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7838979959487915},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.7080978751182556},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6323227286338806},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.595583975315094},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.56538987159729},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5203194618225098},{"id":"https://openalex.org/keywords/snapshot","display_name":"Snapshot (computer storage)","score":0.5135095715522766},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4757218658924103},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.45281144976615906},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.41254955530166626},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2659071087837219},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2576681971549988},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.20719295740127563}],"concepts":[{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.9336698651313782},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7838979959487915},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.7080978751182556},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6323227286338806},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.595583975315094},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.56538987159729},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5203194618225098},{"id":"https://openalex.org/C55282118","wikidata":"https://www.wikidata.org/wiki/Q252683","display_name":"Snapshot (computer storage)","level":2,"score":0.5135095715522766},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4757218658924103},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.45281144976615906},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.41254955530166626},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2659071087837219},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2576681971549988},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.20719295740127563},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"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":"D020869","descriptor_name":"Gene Expression Profiling","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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw624","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw624","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/447/25416915/btw624.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:28171615","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28171615","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:europepmc.org:5032446","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6075080","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/btw624","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw624","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/447/25416915/btw624.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":[],"awards":[{"id":"https://openalex.org/G2772313948","display_name":null,"funder_award_id":"T32HL094294","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3394774020","display_name":null,"funder_award_id":"R01NS079433","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4928678543","display_name":null,"funder_award_id":"T32 HL094294","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7467089314","display_name":null,"funder_award_id":"R01 NS079433","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G8559418104","display_name":"The Molecular Fingerprint of Endothelial Dysfunction","funder_award_id":"15POST25710234","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"}],"funders":[{"id":"https://openalex.org/F4320306230","display_name":"American Heart Association","ror":"https://ror.org/013kjyp64"},{"id":"https://openalex.org/F4320309233","display_name":"Oregon Health and Science University","ror":"https://ror.org/009avj582"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2527533149.pdf","grobid_xml":"https://content.openalex.org/works/W2527533149.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1617495083","https://openalex.org/W1828697400","https://openalex.org/W2026935410","https://openalex.org/W2098339479","https://openalex.org/W2109288169","https://openalex.org/W2137526110","https://openalex.org/W2178294617","https://openalex.org/W2190954851","https://openalex.org/W2271773999","https://openalex.org/W2582743722","https://openalex.org/W6685492720"],"related_works":["https://openalex.org/W2944823289","https://openalex.org/W2542847180","https://openalex.org/W3037018281","https://openalex.org/W2972592048","https://openalex.org/W2358319515","https://openalex.org/W4321854979","https://openalex.org/W2003209439","https://openalex.org/W2497626292","https://openalex.org/W4312214821","https://openalex.org/W2367815957"],"abstract_inverted_index":{"Summary:":[0],"Transcriptional":[1],"profiling":[2,36],"using":[3],"RNA":[4],"sequencing":[5],"(RNAseq)":[6],"has":[7,85,149],"emerged":[8],"as":[9,99],"a":[10,39,94,100],"powerful":[11],"methodology":[12],"to":[13,25,59,90,131,162],"quantify":[14],"global":[15],"gene":[16],"expression":[17],"patterns":[18],"in":[19,42,81,124],"various":[20],"contexts":[21],"from":[22],"single":[23],"cells":[24],"whole":[26],"tissues.":[27],"The":[28,152],"tremendous":[29],"amount":[30],"of":[31,44,106],"data":[32,53,107],"generated":[33],"by":[34],"this":[35],"technology":[37],"presents":[38],"daunting":[40],"challenge":[41],"terms":[43],"effectively":[45],"visualizing":[46],"and":[47,51,63,88,110,113,126],"interpreting":[48],"results.":[49],"Convenient":[50],"intuitive":[52],"interfaces":[54],"are":[55],"critical":[56],"for":[57,117,160],"researchers":[58,109,161],"easily":[60],"upload,":[61],"analyze":[62],"visualize":[64],"their":[65,165],"RNAseq":[66],"data.":[67,166],"We":[68],"designed":[69],"the":[70,86,118,136],"START":[71,119,153],"(Shiny":[72],"Transcriptome":[73],"Analysis":[74],"Resource":[75],"Tool)":[76],"App":[77,120,154],"with":[78,135],"these":[79],"requirements":[80],"mind.":[82],"This":[83],"application":[84],"power":[87],"flexibility":[89],"be":[91,128,143],"resident":[92],"on":[93,145,158],"local":[95],"computer":[96],"or":[97],"serve":[98],"web-based":[101],"environment,":[102],"enabling":[103],"easy":[104],"sharing":[105],"between":[108],"collaborators.":[111],"Availability":[112],"Implementation:":[114],"Source":[115],"Code":[116],"is":[121,155],"written":[122],"entirely":[123],"R":[125,150],"can":[127,142],"freely":[129],"available":[130],"download":[132],"at":[133],"https://github.com/jminnier/STARTapp":[134],"code":[137],"licensed":[138],"under":[139],"GPLv3.":[140],"It":[141],"launched":[144],"any":[146],"system":[147],"that":[148],"installed.":[151],"also":[156],"hosted":[157],"https://kcvi.shinyapps.io/START":[159],"temporarily":[163],"upload":[164],"Contact:":[167],"minnier@ohsu.edu":[168]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":18},{"year":2019,"cited_by_count":16},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2025-10-10T00:00:00"}
