{"id":"https://openalex.org/W4386463918","doi":"https://doi.org/10.1093/bioinformatics/btad547","title":"PyDESeq2: a python package for bulk RNA-seq differential expression analysis","display_name":"PyDESeq2: a python package for bulk RNA-seq differential expression analysis","publication_year":2023,"publication_date":"2023-09-01","ids":{"openalex":"https://openalex.org/W4386463918","doi":"https://doi.org/10.1093/bioinformatics/btad547","pmid":"https://pubmed.ncbi.nlm.nih.gov/37669147"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad547","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad547","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad547/51359184/btad547.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad547/51359184/btad547.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004431423","display_name":"Boris Muzellec","orcid":"https://orcid.org/0000-0002-1035-7017"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Boris Muzellec","raw_affiliation_strings":["Owkin France , Paris, 75009, France"],"affiliations":[{"raw_affiliation_string":"Owkin France , Paris, 75009, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082946945","display_name":"Maria Tele\u0144czuk","orcid":"https://orcid.org/0000-0003-1311-1634"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maria Tele\u0144czuk","raw_affiliation_strings":["Owkin France , Paris, 75009, France"],"affiliations":[{"raw_affiliation_string":"Owkin France , Paris, 75009, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053090823","display_name":"Vincent Cabeli","orcid":"https://orcid.org/0000-0003-0818-2518"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vincent Cabeli","raw_affiliation_strings":["Owkin France , Paris, 75009, France"],"affiliations":[{"raw_affiliation_string":"Owkin France , Paris, 75009, France","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035065022","display_name":"Mathieu Andreux","orcid":"https://orcid.org/0000-0001-5778-9979"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mathieu Andreux","raw_affiliation_strings":["Owkin France , Paris, 75009, France"],"affiliations":[{"raw_affiliation_string":"Owkin France , Paris, 75009, France","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5004431423"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":75.6929,"has_fulltext":true,"cited_by_count":323,"citation_normalized_percentile":{"value":0.99958261,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"39","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9940000176429749,"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":0.9915000200271606,"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/python","display_name":"Python (programming language)","score":0.9451836347579956},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.8596651554107666},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7573235630989075},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7140469551086426},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.7053152322769165},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.6195070147514343},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.563916027545929},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.46729758381843567},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.44784536957740784},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.442058265209198},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4113466143608093},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40897136926651},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.32652053236961365},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.275090754032135},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.23060843348503113}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9451836347579956},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.8596651554107666},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7573235630989075},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7140469551086426},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.7053152322769165},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.6195070147514343},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.563916027545929},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.46729758381843567},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.44784536957740784},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.442058265209198},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4113466143608093},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40897136926651},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.32652053236961365},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.275090754032135},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23060843348503113}],"mesh":[{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad547","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad547","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad547/51359184/btad547.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37669147","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37669147","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:10502239","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10502239","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10502239/pdf/btad547.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad547","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad547","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad547/51359184/btad547.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4386463918.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W2179438025","https://openalex.org/W2800392236","https://openalex.org/W2950221693","https://openalex.org/W2963367647","https://openalex.org/W3003257820","https://openalex.org/W3103145119","https://openalex.org/W4210583065","https://openalex.org/W4362737480"],"related_works":["https://openalex.org/W4294955967","https://openalex.org/W4287789247","https://openalex.org/W3021400038","https://openalex.org/W4311938462","https://openalex.org/W2566205467","https://openalex.org/W4226323523","https://openalex.org/W4386463918","https://openalex.org/W4229450551","https://openalex.org/W4311683883","https://openalex.org/W2020328473"],"abstract_inverted_index":{"PyDESeq2":[0,24],"is":[1,14,25],"released":[2],"as":[3],"an":[4],"open-source":[5],"software":[6],"under":[7],"the":[8,28],"MIT":[9],"license.":[10],"The":[11],"source":[12],"code":[13],"available":[15],"on":[16],"GitHub":[17],"at":[18,22],"https://github.com/owkin/PyDESeq2":[19],"and":[20],"documented":[21],"https://pydeseq2.readthedocs.io.":[23],"part":[26],"of":[27],"scverse":[29],"ecosystem.":[30]},"counts_by_year":[{"year":2026,"cited_by_count":57},{"year":2025,"cited_by_count":170},{"year":2024,"cited_by_count":84},{"year":2023,"cited_by_count":12}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
