{"id":"https://openalex.org/W2098849734","doi":"https://doi.org/10.1093/nar/gkq448","title":"rQuant.web: a tool for RNA-Seq-based transcript quantitation","display_name":"rQuant.web: a tool for RNA-Seq-based transcript quantitation","publication_year":2010,"publication_date":"2010-06-15","ids":{"openalex":"https://openalex.org/W2098849734","doi":"https://doi.org/10.1093/nar/gkq448","mag":"2098849734","pmid":"https://pubmed.ncbi.nlm.nih.gov/20551130"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq448","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq448","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W348/3886819/gkq448.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W348/3886819/gkq448.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090404774","display_name":"Regina Bohnert","orcid":null},"institutions":[{"id":"https://openalex.org/I4210147862","display_name":"Friedrich Miescher Laboratory","ror":"https://ror.org/04vh1tq58","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210147862"]},{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"funder","lineage":["https://openalex.org/I149899117"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"R. Bohnert","raw_affiliation_strings":["Friedrich Miescher Laboratory of the Max Planck Society, T\u00fcbingen, Germany. regina.bohnert@tuebingen.mpg.de","Friedrich Miescher Laboratory of the Max Planck Society, T\u00fcbingen, Germany#TAB#"],"affiliations":[{"raw_affiliation_string":"Friedrich Miescher Laboratory of the Max Planck Society, T\u00fcbingen, Germany. regina.bohnert@tuebingen.mpg.de","institution_ids":["https://openalex.org/I4210147862"]},{"raw_affiliation_string":"Friedrich Miescher Laboratory of the Max Planck Society, T\u00fcbingen, Germany#TAB#","institution_ids":["https://openalex.org/I149899117"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035416263","display_name":"Gunnar R\u00e4tsch","orcid":"https://orcid.org/0000-0001-5486-8532"},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"funder","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210147862","display_name":"Friedrich Miescher Laboratory","ror":"https://ror.org/04vh1tq58","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210147862"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"G. Ratsch","raw_affiliation_strings":["Friedrich Miescher Laboratory of the Max Planck Society, T\u00ef\u00bf\u00bdbingen, Germany"],"affiliations":[{"raw_affiliation_string":"Friedrich Miescher Laboratory of the Max Planck Society, T\u00ef\u00bf\u00bdbingen, Germany","institution_ids":["https://openalex.org/I4210147862","https://openalex.org/I149899117"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5090404774"],"corresponding_institution_ids":["https://openalex.org/I149899117","https://openalex.org/I4210147862"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.6081,"has_fulltext":true,"cited_by_count":73,"citation_normalized_percentile":{"value":0.95525289,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"Web Server","first_page":"W348","last_page":"W351"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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/T11482","display_name":"RNA modifications and cancer","score":0.9991000294685364,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9988999962806702,"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/biology","display_name":"Biology","score":0.8810122013092041},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6069053411483765},{"id":"https://openalex.org/keywords/login","display_name":"Login","score":0.5888597965240479},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4882393181324005},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.444828063249588},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.430440753698349},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4225746989250183},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3562448024749756},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.29071709513664246},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2555469870567322},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14958146214485168},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.12937766313552856}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8810122013092041},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6069053411483765},{"id":"https://openalex.org/C113324615","wikidata":"https://www.wikidata.org/wiki/Q472302","display_name":"Login","level":2,"score":0.5888597965240479},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4882393181324005},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.444828063249588},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.430440753698349},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4225746989250183},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3562448024749756},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.29071709513664246},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2555469870567322},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14958146214485168},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.12937766313552856},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkq448","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq448","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W348/3886819/gkq448.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:20551130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20551130","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:edoc.mpg.de:536300","is_oa":false,"landing_page_url":"http://edoc.mpg.de/536300","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nuclear Acids Research, v.38, 348-351 (2010)","raw_type":"Article"},{"id":"pmh:oai:open-archive.highwire.org:nar:38/suppl_2/W348","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/38/suppl_2/W348","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:2896134","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2896134","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkq448","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq448","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W348/3886819/gkq448.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2098849734.pdf","grobid_xml":"https://content.openalex.org/works/W2098849734.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1583240815","https://openalex.org/W1968475238","https://openalex.org/W1981509058","https://openalex.org/W1996542013","https://openalex.org/W2025964719","https://openalex.org/W2042415836","https://openalex.org/W2086323500","https://openalex.org/W2100448568","https://openalex.org/W2104139298","https://openalex.org/W2107564978","https://openalex.org/W2108234281","https://openalex.org/W2120293208","https://openalex.org/W2129264270","https://openalex.org/W2131088968","https://openalex.org/W2134786821","https://openalex.org/W2134924833","https://openalex.org/W2154431984","https://openalex.org/W2154537630","https://openalex.org/W2161645441"],"related_works":["https://openalex.org/W4256170434","https://openalex.org/W4235220108","https://openalex.org/W4315650027","https://openalex.org/W4238894392","https://openalex.org/W2357607877","https://openalex.org/W4230461295","https://openalex.org/W4311722428","https://openalex.org/W4252054168","https://openalex.org/W4237984244","https://openalex.org/W1971332228"],"abstract_inverted_index":{"We":[0],"provide":[1],"a":[2,64,67],"novel":[3],"web":[4],"service,":[5],"called":[6],"rQuant.web,":[7],"allowing":[8],"convenient":[9],"access":[10],"to":[11,56,81],"tools":[12],"for":[13],"quantitative":[14],"analysis":[15],"of":[16,76],"RNA":[17],"sequencing":[18,38],"data.":[19],"The":[20],"underlying":[21],"quantitation":[22],"technique":[23],"rQuant":[24],"is":[25,51,61,74,79,86],"based":[26],"on":[27],"quadratic":[28],"programming":[29],"and":[30,39,50,84],"estimates":[31],"different":[32],"biases":[33],"induced":[34],"by":[35],"library":[36],"preparation,":[37],"read":[40],"mapping.":[41],"It":[42],"can":[43],"tackle":[44],"multiple":[45],"transcripts":[46],"per":[47],"gene":[48],"locus":[49],"therefore":[52],"particularly":[53],"well":[54],"suited":[55],"quantify":[57],"alternative":[58],"transcripts.":[59],"rQuant.web":[60,73],"available":[62],"as":[63],"tool":[65],"in":[66],"Galaxy":[68],"installation":[69],"at":[70],"http://galaxy.fml.mpg.de.":[71],"Using":[72],"free":[75],"charge,":[77],"it":[78],"open":[80],"all":[82],"users,":[83],"there":[85],"no":[87],"login":[88],"requirement.":[89]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":11}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
