{"id":"https://openalex.org/W25727073","doi":null,"title":"Analysing RNA-Seq data with the DESeq package","display_name":"Analysing RNA-Seq data with the DESeq package","publication_year":2011,"publication_date":"2011-01-01","ids":{"openalex":"https://openalex.org/W25727073","mag":"25727073"},"language":"en","primary_location":{"id":"mag:25727073","doi":null,"is_oa":false,"landing_page_url":"https://bioc.ism.ac.jp/packages/2.10/bioc/vignettes/DESeq/inst/doc/DESeq.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022280742","display_name":"Simon Anders","orcid":"https://orcid.org/0000-0003-4868-1805","observed_orcids":["https://orcid.org/0000-0003-4868-1805"]},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Simon Anders","raw_affiliation_strings":["Technical University of Munich"],"raw_orcid":"https://orcid.org/0000-0003-4868-1805","affiliations":[{"raw_affiliation_string":"Technical University of Munich","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5022280742"],"corresponding_institution_ids":["https://openalex.org/I62916508"],"apc_list":null,"apc_paid":null,"fwci":1.2839,"has_fulltext":false,"cited_by_count":163,"citation_normalized_percentile":{"value":0.77129569,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8955000042915344,"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":0.8955000042915344,"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":0.08299999684095383,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.011500000022351742,"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/deseq","display_name":"DESeq","score":0.7760000228881836},{"id":"https://openalex.org/keywords/differential-gene-expression","display_name":"differential gene expression","score":0.828000009059906},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-seq","score":0.8889999985694885},{"id":"https://openalex.org/keywords/count-data","display_name":"count data","score":0.9340000152587891},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6480000019073486},{"id":"https://openalex.org/keywords/chip-seq","display_name":"ChIP-seq","score":0.7260000109672546},{"id":"https://openalex.org/keywords/statistical-significance-testing","display_name":"statistical significance testing","score":0.4569999873638153}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6732208132743835},{"id":"https://openalex.org/C33643355","wikidata":"https://www.wikidata.org/wiki/Q5176731","display_name":"Count data","level":3,"score":0.5973156690597534},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5807644724845886},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.5394760966300964},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.47817546129226685},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4689333736896515},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34834200143814087},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3314053416252136},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18540877103805542},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17493313550949097},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1713414490222931},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1547473669052124},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12200483679771423},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.10616344213485718},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08681297302246094},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.07587921619415283},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:25727073","doi":null,"is_oa":false,"landing_page_url":"https://bioc.ism.ac.jp/packages/2.10/bioc/vignettes/DESeq/inst/doc/DESeq.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3358182130","display_name":"Critical Role for Microvasculature in Airway Transplantation","funder_award_id":"R01HL095686","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G4280569226","display_name":"Airway redox biochemistry as a deteriminant of asthma phenotype during adolescen*","funder_award_id":"U10HL109250","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6426351722","display_name":null,"funder_award_id":"P01-HL-108797","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6999456363","display_name":null,"funder_award_id":"I01 BX000509","funder_id":"https://openalex.org/F4320306127","funder_display_name":"U.S. Department of Veterans Affairs"},{"id":"https://openalex.org/G7366038496","display_name":"Pulmonary Hypertension Breakthrough Initiative","funder_award_id":"R24HL123767","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G986298929","display_name":null,"funder_award_id":"1P01HL108797","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320306127","display_name":"U.S. Department of Veterans Affairs","ror":"https://ror.org/05rsv9s98"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W147963563","https://openalex.org/W2020943639","https://openalex.org/W2058358568","https://openalex.org/W2064129461","https://openalex.org/W2152239989","https://openalex.org/W2155115337"],"related_works":["https://openalex.org/W7097043320","https://openalex.org/W7099866208","https://openalex.org/W2189254770","https://openalex.org/W7095960161","https://openalex.org/W7097249212","https://openalex.org/W2179438025","https://openalex.org/W2152239989","https://openalex.org/W7098470987","https://openalex.org/W651062373","https://openalex.org/W2119034410"],"abstract_inverted_index":{"Abstract":[0],"A":[1],"basic":[2],"task":[3],"in":[4],"the":[5,13,32,73,78,81,87],"analysis":[6],"of":[7,15,34,68,80,86],"count":[8,20],"data":[9,21],"from":[10],"RNA-Seq":[11],"is":[12],"detection":[14],"differentially":[16],"expressed":[17],"genes.":[18],"The":[19,55],"are":[22],"presented":[23],"as":[24,52],"a":[25,41,59,69],"table":[26],"which":[27],"reports,":[28],"for":[29,47,63,72],"each":[30],"sample,":[31],"number":[33],"reads":[35],"that":[36],"have":[37],"been":[38],"assigned":[39],"to":[40,61],"gene.":[42],"Analogous":[43],"analyses":[44],"also":[45],"arise":[46],"other":[48],"assay":[49],"types,":[50],"such":[51],"comparative":[53],"ChIP-Seq.":[54],"package":[56],"DESeq":[57],"provides":[58],"method":[60,89],"test":[62],"differential":[64],"expression":[65],"by":[66],"use":[67,79],"shrinkage":[70],"estimtor":[71],"variance.":[74],"This":[75],"vignette":[76],"explains":[77],"package.":[82],"For":[83],"an":[84],"exposition":[85],"statistical":[88],"employed,":[90],"please":[91],"see":[92],"our":[93],"paper":[94],"[1].":[95]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":23},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}