{"id":"https://openalex.org/W7219607396","doi":"https://doi.org/10.5281/zenodo.23123980","title":"Analysis package for A detectability floor for treatment-response labels in rheumatology transcriptomics","display_name":"Analysis package for A detectability floor for treatment-response labels in rheumatology transcriptomics","publication_year":2026,"publication_date":"2026-10-03","ids":{"openalex":"https://openalex.org/W7219607396","doi":"https://doi.org/10.5281/zenodo.23123980"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.23123980","doi":"https://doi.org/10.5281/zenodo.23123980","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23123980","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"volume":null,"type":"software","is_traditional":false,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.23123980","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5157128564","display_name":"Haitao Yang","orcid":"https://orcid.org/0009-0006-6148-6018","observed_orcids":["https://orcid.org/0009-0006-6148-6018"]},"institutions":[{"id":"https://openalex.org/I4210105608","display_name":"ShenZhen People\u2019s Hospital","ror":"https://ror.org/01hcefx46","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210105608"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang, Haitao","raw_affiliation_strings":["Department of Rheumatology and Immunology, People's Hospital of Longhua, Shenzhen, Guangdong 518109, P.R. China"],"raw_orcid":"https://orcid.org/0009-0006-6148-6018","affiliations":[{"raw_affiliation_string":"Department of Rheumatology and Immunology, People's Hospital of Longhua, Shenzhen, Guangdong 518109, P.R. China","institution_ids":["https://openalex.org/I4210105608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5157130063","display_name":"Yan Huang","orcid":"https://orcid.org/0009-0007-7067-5416","observed_orcids":["https://orcid.org/0009-0007-7067-5416"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huang, Yan","raw_affiliation_strings":["Department of Internal Medicine, Kuichong People's Hospital, Shenzhen, Guangdong 518119, P.R. China"],"raw_orcid":"https://orcid.org/0009-0007-7067-5416","affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Kuichong People's Hospital, Shenzhen, Guangdong 518119, P.R. China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5156893074","display_name":"Jianghua Xu","orcid":"https://orcid.org/0009-0005-9737-7086","observed_orcids":["https://orcid.org/0009-0005-9737-7086"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xu, Jianghua","raw_affiliation_strings":["Department of Medical Service for Special Forces, General Hospital of Southern Theater Command, Guangzhou, Guangdong 510010, P.R. China"],"raw_orcid":"https://orcid.org/0009-0005-9737-7086","affiliations":[{"raw_affiliation_string":"Department of Medical Service for Special Forces, General Hospital of Southern Theater Command, Guangzhou, Guangdong 510010, P.R. China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014846025","display_name":"Suo Zhang","orcid":"https://orcid.org/0009-0004-9602-7634","observed_orcids":["https://orcid.org/0009-0004-9602-7634"]},"institutions":[{"id":"https://openalex.org/I4210164332","display_name":"Shenzhen Second People's Hospital","ror":"https://ror.org/05c74bq69","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164332"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhang, Suo","raw_affiliation_strings":["Department of Rheumatology and Immunology, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518032, P.R. China"],"raw_orcid":"https://orcid.org/0009-0004-9602-7634","affiliations":[{"raw_affiliation_string":"Department of Rheumatology and Immunology, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518032, P.R. China","institution_ids":["https://openalex.org/I4210164332"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5126165887","display_name":"Rui Liao","orcid":"https://orcid.org/0000-0001-7529-6377","observed_orcids":["https://orcid.org/0000-0001-7529-6377"]},"institutions":[{"id":"https://openalex.org/I4210133784","display_name":"First Affiliated Hospital of Gannan Medical University","ror":"https://ror.org/040gnq226","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210133784"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liao, Rui","raw_affiliation_strings":["Department of Rheumatology and Immunology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China"],"raw_orcid":"https://orcid.org/0000-0001-7529-6377","affiliations":[{"raw_affiliation_string":"Department of Rheumatology and Immunology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China","institution_ids":["https://openalex.org/I4210133784"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"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":0.350600004196167,"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":0.350600004196167,"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/T10206","display_name":"Meta-analysis and systematic reviews","score":0.05829999968409538,"subfield":{"id":"https://openalex.org/subfields/1804","display_name":"Statistics, Probability and Uncertainty"},"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/T11937","display_name":"Research Data Management Practices","score":0.05469999834895134,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/juvenile-dermatomyositis","display_name":"juvenile dermatomyositis","score":0.6959999799728394},{"id":"https://openalex.org/keywords/rheumatoid-arthritis","display_name":"rheumatoid arthritis","score":0.9940000176429749},{"id":"https://openalex.org/keywords/methotrexate","display_name":"methotrexate","score":0.9739999771118164},{"id":"https://openalex.org/keywords/lupus-nephritis","display_name":"lupus nephritis","score":0.9929999709129333}],"concepts":[{"id":"https://openalex.org/C204434341","wikidata":"https://www.wikidata.org/wiki/Q357789","display_name":"Adjudication","level":2,"score":0.7257000207901001},{"id":"https://openalex.org/C199521495","wikidata":"https://www.wikidata.org/wiki/Q181487","display_name":"Audit","level":2,"score":0.6721000075340271},{"id":"https://openalex.org/C2776213154","wikidata":"https://www.wikidata.org/wiki/Q13370881","display_name":"Verdict","level":2,"score":0.6078000068664551},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5394999980926514},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4537000060081482},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.42480000853538513},{"id":"https://openalex.org/C2776119841","wikidata":"https://www.wikidata.org/wiki/Q837675","display_name":"Jury","level":2,"score":0.40070000290870667},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.390500009059906},{"id":"https://openalex.org/C72563966","wikidata":"https://www.wikidata.org/wiki/Q1303415","display_name":"Cohort","level":2,"score":0.38199999928474426},{"id":"https://openalex.org/C175291020","wikidata":"https://www.wikidata.org/wiki/Q1156822","display_name":"Offset (computer science)","level":2,"score":0.37959998846054077},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.36000001430511475},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3476000130176544},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.3321000039577484},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33160001039505005},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.3206000030040741},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.3172999918460846},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.2994999885559082},{"id":"https://openalex.org/C2778217198","wikidata":"https://www.wikidata.org/wiki/Q556977","display_name":"Cutoff","level":2,"score":0.29600000381469727},{"id":"https://openalex.org/C2780315633","wikidata":"https://www.wikidata.org/wiki/Q16354","display_name":"Whiteboard","level":2,"score":0.2957000136375427},{"id":"https://openalex.org/C59577422","wikidata":"https://www.wikidata.org/wiki/Q10265143","display_name":"False accusation","level":2,"score":0.2831999957561493},{"id":"https://openalex.org/C102366305","wikidata":"https://www.wikidata.org/wiki/Q1097688","display_name":"Nonparametric statistics","level":2,"score":0.2791999876499176},{"id":"https://openalex.org/C28490314","wikidata":"https://www.wikidata.org/wiki/Q189436","display_name":"Speech recognition","level":1,"score":0.27399998903274536},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.26899999380111694},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.26840001344680786},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2623000144958496}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5281/zenodo.23123980","doi":"https://doi.org/10.5281/zenodo.23123980","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23123980","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},{"id":"doi:10.5281/zenodo.23123981","doi":"https://doi.org/10.5281/zenodo.23123981","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23123981","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"}],"best_oa_location":{"id":"doi:10.5281/zenodo.23123980","doi":"https://doi.org/10.5281/zenodo.23123980","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23123980","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"sustainable_development_goals":[{"score":0.8048999905586243,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7220704494","https://openalex.org/W7223383866","https://openalex.org/W7203776241","https://openalex.org/W7169874567","https://openalex.org/W6963131409","https://openalex.org/W2986835752","https://openalex.org/W2972578946","https://openalex.org/W7220976762","https://openalex.org/W2783228590","https://openalex.org/W7014154261"],"abstract_inverted_index":{"Deposit":[0],"for":[1,7,38,83,91],"the":[2,39,56,66,86,114,123,173,224,229],"manuscript":[3],"\"A":[4],"detectability":[5,174],"floor":[6],"treatment-response":[8],"labels":[9,62],"inrheumatology":[10],"transcriptomics\".":[11],"The":[12],"archive":[13],"contains":[14],"everything":[15],"needed":[16],"to":[17,76],"reproduce":[18],"thereported":[19],"numbers":[20],"from":[21,64,142],"public":[22],"input":[23],"data;":[24],"no":[25,31],"new":[26],"data":[27,36],"were":[28],"generated":[29],"and":[30,51,68,88,110,122,208,219,244],"controlled-accessmaterial":[32],"was":[33,164,169,189,194],"used.":[34],"Contents:":[35],"provenance":[37],"extended":[40],"label":[41,49,178],"audit":[42,58],"(platform,":[43],"annotation":[44],"priority,":[45],"genecoverage,":[46],"retrieval":[47],"date,":[48],"field":[50,202],"mapping":[52],"rule,":[53],"deposited-versus-published":[54],"group-sizecomparison);":[55],"pre-registered":[57],"protocol;":[59],"per-sample":[60],"response":[61],"recovered":[63],"eachdeposit;":[65],"screening":[67,215],"adjudication":[69,217],"ledgers":[70],"taking":[71],"45":[72],"auditable":[73],"papers":[74],"down":[75],"15":[77],"auditedcohorts,":[78],"with":[79,239],"a":[80,105,148,154,161,176],"registered":[81,165],"reason":[82],"every":[84,245],"exclusion;":[85],"analysis":[87,188,220],"plotting":[89],"code":[90],"theprimary":[92],"cohorts":[93],"(juvenile":[94],"dermatomyositis,":[95],"rheumatoid":[96],"arthritis":[97],"before/after":[98],"methotrexate,lupus":[99],"nephritis,":[100],"two":[101],"controlled":[102],"glucocorticoid":[103],"challenges,":[104],"single-cell":[106],"dose":[107],"series),":[108],"thegender-composition":[109],"per-gene":[111],"stability":[112],"checks,":[113],"score-level":[115],"injection":[116],"calibration":[117],"andthe":[118],"attainable-AUC":[119],"ceiling":[120],"analysis;":[121],"corresponding":[124],"result":[125,150],"files.":[126],"Design":[127],"floors":[128],"are":[129,211,222],"exact":[130],"non-central-t":[131],"minima":[132],"(80%":[133],"power,":[134],"two-sided":[135],"alpha":[136],"=":[137],"0.05)":[138],"computed":[139],"foreach":[140],"cohort":[141],"its":[143,236],"own":[144],"group":[145],"sizes,":[146],"so":[147],"negative":[149],"is":[151,182,233],"reported":[152],"as":[153,179],"bound":[155],"rather":[156],"thanan":[157],"absence.":[158],"Verdicts":[159],"follow":[160],"taxonomy":[162],"that":[163,185],"before":[166],"any":[167,186],"verdict":[168,171,206],"computed.A":[170],"characterises":[172],"of":[175],"supervision":[177],"deposited;":[180],"it":[181],"not":[183],"aclaim":[184],"published":[187],"erroneous.":[190],"No":[191],"virtual-cell":[192],"model":[193],"evaluated":[195],"in":[196,212,223,235,248],"thiswork.":[197],"Language":[198],"convention:":[199],"file":[200],"names,":[201,203],"column":[204],"headers,":[205],"codes":[207],"all":[209],"numericoutput":[210],"English.":[213],"Recorded":[214],"reasons,":[216],"notes":[218],"logannotations":[221],"authors'":[225],"working":[226],"language":[227],"(Chinese);":[228],"full":[230],"PRISMA-style":[231],"screeningrecord":[232],"deposited":[234],"original":[237],"form":[238],"an":[240],"English":[241],"summary":[242],"prepended,":[243],"ledgeris":[246],"described":[247],"ledgers/README_ledgers.md.":[249]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-10-05T00:00:00"}
