{"id":"https://openalex.org/W7124542484","doi":"https://doi.org/10.5281/zenodo.18280972","title":"UNITE software","display_name":"UNITE software","publication_year":2026,"publication_date":"2026-01-17","ids":{"openalex":"https://openalex.org/W7124542484","doi":"https://doi.org/10.5281/zenodo.18280972"},"language":null,"primary_location":{"id":"doi:10.5281/zenodo.18280972","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.18280972","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,"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"},"type":"software","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.18280972","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5123286788","display_name":"Haichao Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Haichao","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-7648-916X","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Mennea, Paulius Danielius","orcid":"https://orcid.org/0000-0002-6967-1975"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mennea, Paulius Danielius","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-6967-1975","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Mc Andrew, Grainne","orcid":"https://orcid.org/0000-0002-9885-0294"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mc Andrew, Grainne","raw_affiliation_strings":["Queen Mary University of London"],"raw_orcid":"https://orcid.org/0000-0002-9885-0294","affiliations":[{"raw_affiliation_string":"Queen Mary University of London","institution_ids":["https://openalex.org/I166337079"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sonmezler, Ozge","orcid":"https://orcid.org/0000-0002-2757-718X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sonmezler, Ozge","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-2757-718X","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Shcherbo, Dmitry","orcid":"https://orcid.org/0000-0002-0266-7015"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shcherbo, Dmitry","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-0266-7015","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Ditter, Emma-Jane","orcid":"https://orcid.org/0000-0003-0625-7264"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ditter, Emma-Jane","raw_affiliation_strings":["University of Cambridge"],"raw_orcid":"https://orcid.org/0000-0003-0625-7264","affiliations":[{"raw_affiliation_string":"University of Cambridge","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":null,"display_name":"\u00d8strup Jensen, Sarah","orcid":"https://orcid.org/0000-0001-6044-3362"},"institutions":[{"id":"https://openalex.org/I204337017","display_name":"Aarhus University","ror":"https://ror.org/01aj84f44","country_code":"DK","type":"education","lineage":["https://openalex.org/I204337017"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2801316944"]}],"countries":["DK","GB"],"is_corresponding":false,"raw_author_name":"\u00d8strup Jensen, Sarah","raw_affiliation_strings":["Aarhus University","Cancer Research UK Cambridge Institute, University of Cambridge"],"raw_orcid":"https://orcid.org/0000-0001-6044-3362","affiliations":[{"raw_affiliation_string":"Aarhus University","institution_ids":["https://openalex.org/I204337017"]},{"raw_affiliation_string":"Cancer Research UK Cambridge Institute, University of Cambridge","institution_ids":["https://openalex.org/I241749","https://openalex.org/I2801316944"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Buma, Alessandra Ida Giuseppina","orcid":"https://orcid.org/0009-0003-7896-9890"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I2802849423","display_name":"University Medical Center","ror":"https://ror.org/036pt7h44","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2802849423"]},{"id":"https://openalex.org/I2802934949","display_name":"Radboud University Medical Center","ror":"https://ror.org/05wg1m734","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2802934949"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Buma, Alessandra Ida Giuseppina","raw_affiliation_strings":["Radboud University Medical Center"],"raw_orcid":"https://orcid.org/0009-0003-7896-9890","affiliations":[{"raw_affiliation_string":"Radboud University Medical Center","institution_ids":["https://openalex.org/I145872427","https://openalex.org/I2802849423","https://openalex.org/I2802934949"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Smith, Christopher","orcid":"https://orcid.org/0000-0001-7357-2737"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Smith, Christopher","raw_affiliation_strings":["University of Cambridge"],"raw_orcid":"https://orcid.org/0000-0001-7357-2737","affiliations":[{"raw_affiliation_string":"University of Cambridge","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Cheng, Zhao","orcid":"https://orcid.org/0000-0002-3514-240X"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Cheng, Zhao","raw_affiliation_strings":["University of Cambridge"],"raw_orcid":"https://orcid.org/0000-0002-3514-240X","affiliations":[{"raw_affiliation_string":"University of Cambridge","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Harris, Clare","orcid":"https://orcid.org/0000-0002-5560-5344"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Harris, Clare","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-5560-5344","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Cutts, Rosalind","orcid":"https://orcid.org/0000-0002-8297-9341"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cutts, Rosalind","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-8297-9341","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Hrebien, Sarah","orcid":"https://orcid.org/0009-0000-9121-8299"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hrebien, Sarah","raw_affiliation_strings":["Institute of Cancer Research"],"raw_orcid":"https://orcid.org/0009-0000-9121-8299","affiliations":[{"raw_affiliation_string":"Institute of Cancer Research","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Crosbie, Phil","orcid":"https://orcid.org/0000-0001-8941-4813"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4210092852","display_name":"Manchester University NHS Foundation Trust","ror":"https://ror.org/00he80998","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210092852"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Crosbie, Phil","raw_affiliation_strings":["University of Manchester","Manchester University NHS Foundation Trust"],"raw_orcid":"https://orcid.org/0000-0001-8941-4813","affiliations":[{"raw_affiliation_string":"University of Manchester","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"Manchester University NHS Foundation Trust","institution_ids":["https://openalex.org/I4210092852"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Corrie, Pippa","orcid":"https://orcid.org/0000-0003-4875-7021"},"institutions":[{"id":"https://openalex.org/I2802466933","display_name":"Cambridge University Hospitals NHS Foundation Trust","ror":"https://ror.org/04v54gj93","country_code":"GB","type":"funder","lineage":["https://openalex.org/I2802466933"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Corrie, Pippa","raw_affiliation_strings":["Cambridge University Hospitals NHS Foundation Trust"],"raw_orcid":"https://orcid.org/0000-0003-4875-7021","affiliations":[{"raw_affiliation_string":"Cambridge University Hospitals NHS Foundation Trust","institution_ids":["https://openalex.org/I2802466933"]}]},{"author_position":"middle","author":{"id":null,"display_name":"van den Heuvel, Michel","orcid":"https://orcid.org/0000-0002-6372-2153"},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]},{"id":"https://openalex.org/I3018483916","display_name":"University Medical Center Utrecht","ror":"https://ror.org/0575yy874","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I3018483916"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"van den Heuvel, Michel","raw_affiliation_strings":["University Medical Center Utrecht","The Netherlands Cancer Institute"],"raw_orcid":"https://orcid.org/0000-0002-6372-2153","affiliations":[{"raw_affiliation_string":"University Medical Center Utrecht","institution_ids":["https://openalex.org/I3018483916"]},{"raw_affiliation_string":"The Netherlands Cancer Institute","institution_ids":["https://openalex.org/I2898336195"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Roshan, Amit","orcid":"https://orcid.org/0000-0002-2034-2759"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802466933","display_name":"Cambridge University Hospitals NHS Foundation Trust","ror":"https://ror.org/04v54gj93","country_code":"GB","type":"funder","lineage":["https://openalex.org/I2802466933"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Roshan, Amit","raw_affiliation_strings":["Cambridge University Hospitals NHS Foundation Trust","University of Cambridge"],"raw_orcid":"https://orcid.org/0000-0002-2034-2759","affiliations":[{"raw_affiliation_string":"Cambridge University Hospitals NHS Foundation Trust","institution_ids":["https://openalex.org/I2802466933"]},{"raw_affiliation_string":"University of Cambridge","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Frank, McCaughan","orcid":"https://orcid.org/0000-0002-8012-7524"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Frank, McCaughan","raw_affiliation_strings":["University of Cambridge"],"raw_orcid":"https://orcid.org/0000-0002-8012-7524","affiliations":[{"raw_affiliation_string":"University of Cambridge","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Rintoul, Robert","orcid":"https://orcid.org/0000-0003-3875-3780"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210104974","display_name":"Papworth Hospital NHS Foundation Trust","ror":"https://ror.org/01qbebb31","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210104974"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rintoul, Robert","raw_affiliation_strings":["University of Cambridge","Papworth Hospital NHS Foundation Trust"],"raw_orcid":"https://orcid.org/0000-0003-3875-3780","affiliations":[{"raw_affiliation_string":"University of Cambridge","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Papworth Hospital NHS Foundation Trust","institution_ids":["https://openalex.org/I4210104974"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Markowetz, Florian","orcid":"https://orcid.org/0000-0002-2784-5308"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Markowetz, Florian","raw_affiliation_strings":["University of Cambridge"],"raw_orcid":"https://orcid.org/0000-0002-2784-5308","affiliations":[{"raw_affiliation_string":"University of Cambridge","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Kaplan, Tommy","orcid":"https://orcid.org/0000-0002-1892-5461"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["GB","IL"],"is_corresponding":false,"raw_author_name":"Kaplan, Tommy","raw_affiliation_strings":["Hebrew University of Jerusalem","queen mary university of london"],"raw_orcid":"https://orcid.org/0000-0002-1892-5461","affiliations":[{"raw_affiliation_string":"Hebrew University of Jerusalem","institution_ids":["https://openalex.org/I197251160"]},{"raw_affiliation_string":"queen mary university of london","institution_ids":["https://openalex.org/I166337079"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Cooper, Wendy Nicola","orcid":"https://orcid.org/0000-0003-3416-9982"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Cooper, Wendy Nicola","raw_affiliation_strings":["University of Cambridge"],"raw_orcid":"https://orcid.org/0000-0003-3416-9982","affiliations":[{"raw_affiliation_string":"University of Cambridge","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhao, Hui","orcid":"https://orcid.org/0009-0009-2818-2911"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Zhao, Hui","raw_affiliation_strings":["Queen Mary University of London"],"raw_orcid":"https://orcid.org/0009-0009-2818-2911","affiliations":[{"raw_affiliation_string":"Queen Mary University of London","institution_ids":["https://openalex.org/I166337079"]}]},{"author_position":"last","author":{"id":null,"display_name":"Rosenfeld, Nitzan","orcid":"https://orcid.org/0000-0002-2825-4788"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rosenfeld, Nitzan","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-2825-4788","affiliations":[]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":14,"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":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.43320000171661377},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.35019999742507935},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.24889999628067017},{"id":"https://openalex.org/keywords/code-of-practice","display_name":"Code of practice","score":0.2206999957561493}],"concepts":[{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.43320000171661377},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.35019999742507935},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3303000032901764},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.24889999628067017},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.2401999980211258},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2321999967098236},{"id":"https://openalex.org/C2992077309","wikidata":"https://www.wikidata.org/wiki/Q55607839","display_name":"Code of practice","level":2,"score":0.2206999957561493},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.20819999277591705},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.19859999418258667},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.19120000302791595}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5281/zenodo.18280972","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.18280972","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,"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":null,"raw_source_name":null,"raw_type":"Software"}],"best_oa_location":{"id":"doi:10.5281/zenodo.18280972","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.18280972","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,"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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"This":[0,109,130,217,250,820,1038],"repository":[1,110],"contains":[2],"the":[3,9,13,22,59,62,66,80,105,186,200,208,235,248,254,260,315,339,347,350,359,371,376,392,421,470,475,494,519,535,557,587,641,647,663,669,707,719,774,779,827,871,875,886,894,910,914,953,957,963,973,1042,1053,1056,1087,1141,1176,1184,1207,1231,1247,1253,1256,1261],"code":[4,486,802,985],"and":[5,28,34,184,263,401,477,485,543,595,633,716,831],"resources":[6,101],"used":[7,140,585,660,898,1250],"in":[8,335,338,375,381,388,398,580,586,591,597,725,847,885,893,909,924,997,1086,1143,1156,1191,1206,1230],"UNITE":[10,36,96,377,797,808,948,970,1036,1057,1257],"paper":[11,378,588],"by":[12,420,437,793,1214,1219,1224],"Rosenfeld":[14],"Group.":[15],"It":[16],"includes":[17],"instructions":[18],"for":[19,75,117,202,488,503,616,631,845,901,922,980,990,995,1045,1075,1082,1233],"setting":[20],"up":[21],"analysis":[23,120],"environment,":[24,115,201,349],"accessing":[25],"raw":[26,89,575],"data":[27,85,90,99,364,369,395,484,576,629,800,811],"extracted":[29,87,573],"features,":[30],"using":[31,134,226,242,331,346,358,417,668,712,731,750,762,773,789],"trained":[32,711],"models,":[33],"running":[35,318],"on":[37,97,121,680,718,798,809,812],"new":[38,98,799,810],"shallow":[39,366],"whole-genome":[40,367],"sequencing":[41,368,832,1199],"data.":[42],"The":[43,136,365,384,394,431,444,483,619,675,688,696,801,878,889,904,984,1094,1103,1118,1236,1243],"codes":[44],"are":[45,379,386,397,402,433,446,487,589,706,897,978,1097],"uploaded":[46],"to":[47,58,64,198,409,500,538,560,646,661,806,874,949,1091,1251],"this":[48,902,1157],"Zenodo":[49,341],"record":[50],"as":[51,257,447,469,514,546,754,765,778,899,913],"a":[52,112,522,530,539,592,628,728,813,838,1072,1079],"3.9GB":[53],"zip":[54],"file":[55,131,496,537,724,729,740,841,873,1081,1089,1133],"(Please":[56],"scroll":[57],"bottom":[60],"of":[61,328,345,370,391,474,829,1035,1105,1128,1140,1148,1175,1183,1203],"page":[63],"see":[65,1227],"files":[67,396,407,432,621,881,891,906,977,1044],"session,":[68],"access":[69],"is":[70,144,152,158,219,333,521,727,1246],"restricted).":[71],"Please":[72,516,1226],"contact":[73],"bci-nrlab-admin@qmul.ac.uk":[74],"access.":[76],"UNITE-paper":[77],"Contents":[78],"Using":[79,104],"pre-built":[81,106,113],"Conda":[82,107,114],"environment":[83,108,137,187,236,249,255,316,351],"Raw":[84,363],"Features":[86,572],"from":[88,193,356,404,574,640,702],"Docker":[91,653,676],"image":[92,654,677],"Trained":[93,694],"models":[94,695,698,710],"Running":[95,796],"Key":[100],"License":[102],"1.":[103],"provides":[111,627],"R4_1.tar.gz,":[116,189],"fully":[118],"reproducible":[119,581],"Linux":[122,128,310],"systems,":[123],"including":[124,826],"HPC":[125],"or":[126,146,150,509,1109,1137],"local":[127],"machines.":[129],"was":[132,659,678,691],"generated":[133,892,979,992],"conda-pack.":[135],"can":[138,352,497,699,1121],"be":[139,354,498,700,843,883,908],"with":[141,435,1255],"micromamba,":[142],"which":[143],"recommended,":[145],"Miniconda.":[147],"If":[148,492],"conda":[149,221,237,859,936,1012],"mamba":[151],"already":[153],"installed,":[154],"no":[155],"additional":[156],"installation":[157],"required.":[159,220],"Install":[160],"micromamba":[161,174,228,244,332],"curl":[162],"-Ls":[163],"https://micro.mamba.pm/api/micromamba/linux-64/latest":[164],"|":[165],"tar":[166,210],"-xvj":[167],"bin/micromamba":[168,171],"chmod":[169],"+x":[170],"export":[172],"PATH=\"$PWD/bin:$PATH\"":[173],"shell":[175],"init":[176],"-s":[177],"bash":[178,965],"-p":[179,205,855,920,932],"~/micromamba":[180],"source":[181],"~/.bashrc":[182],"Download":[183,188],"unpack":[185],"approximately":[190],"3.4":[191],"GB,":[192],"Zenodo:":[194,382,598,703],"https://doi.org/10.5281/zenodo.18187489":[195],"Choose":[196],"where":[197,526],"install":[199],"example:":[203],"mkdir":[204,919],"~/conda_envs/R4_1":[206,214,223,230,239,246],"Unpack":[207],"environment:":[209],"-xzf":[211],"R4_1.tar.gz":[212],"-C":[213],"Fix":[215],"paths":[216],"step":[218,251,821,896,1039],"activate":[222,229,238,245,860,937,1013],"Alternatively,":[224,240],"if":[225,241,322],"micromamba:":[227,243],"Then":[231],"run:":[232,264,1061],"conda-unpack":[233,321],"Activate":[234],"Verify":[247],"verifies":[252],"that":[253,518],"works":[256],"expected.":[258],"Open":[259],"R":[261,541],"console":[262],"library(pacman)":[265],"packages":[266,329],"<-":[267],"c(":[268],"\"parallel\",":[269],"\"future\",":[270],"\"furrr\",":[271],"\"progressr\",":[272],"\"parallelly\",":[273],"\"tidyverse\",":[274],"\"Biobase\",":[275],"\"QDNAseq\",":[276],"\"Homo.sapiens\",":[277],"\"plyranges\",":[278],"\"GenomicRanges\",":[279],"\"GenomicAlignments\",":[280],"\"matrixStats\",":[281],"\"AnnotationHub\",":[282],"\"BSgenome.Hsapiens.UCSC.hg19\",":[283],"\"BSgenome.Hsapiens.UCSC.hg38\",":[284],"\"Rsamtools\",":[285],"\"rslurm\",":[286],"\"abind\",":[287],"\"tictoc\",":[288],"\"patchwork\",":[289],"\"EBImage\",":[290],"\"gridExtra\",":[291],"\"grid\",":[292],"\"reshape2\",":[293],"\"purrr\",":[294],"\"fastDummies\",":[295],"\"ggalluvial\",":[296],"\"MultiAssayExperiment\",":[297],"\"nord\",":[298],"\"plotly\",":[299],"\"htmlwidgets\",":[300],"\"ggpubr\",":[301],"\"argparse\",":[302],"\"argparser\",":[303],"\"bettermc\"":[304],")":[305],"p_load(char":[306],"=":[307],"packages)":[308],"Notes":[309],"only.":[311,491],"Do":[312],"not":[313],"move":[314],"after":[317],"conda-unpack.":[319],"Re-run":[320],"activation":[323],"fails.":[324],"An":[325],"explicit":[326,360],"list":[327],"installed":[330],"provided":[334],"R4_1.explicit.txt,":[336],"deposited":[337,380,596,620],"same":[340,775,911,1119],"record:":[342],"https://doi.org/10.5281/zenodo.18187489.":[343],"Instead":[344],"packed":[348],"also":[353],"built":[355],"scratch":[357],"file.":[361,983,1209],"2.":[362],"newly":[372],"sequenced":[373],"samples":[374,618,715,1077,1153],"https://doi.org/10.5281/zenodo.18155576":[383],"metadata":[385,1095,1254],"recorded":[387],"Table":[389,1228],"S12":[390],"manuscript.":[393],".tsv.gz":[399],"format":[400],"derived":[403],"0.1x":[405],"BAM":[406,501,513,524,561,818,824,836,872,880,905,959,982,1132,1208],"aligned":[408],"hg19.":[410],"Paired":[411],"reads":[412,479,830,1205],"were":[413,1154],"merged":[414],"into":[415],"fragments":[416],"cfDNAPro,":[418],"developed":[419],"lab:":[422],"https://github.com/NRLAB-CRUK/cfDNAPro":[423],"Reference:":[424],"Wang":[425],"et":[426,439],"al.,":[427,440],"Genome":[428],"Biology,":[429],"2021.":[430],"compatible":[434],"FinaleDB":[436],"Zheng":[438],"Bioinformatics,":[441],"2021:":[442],"http://finaledb.research.cchmc.org/":[443],"columns":[445,1096],"follows:":[448],"Column":[449],"Example":[450],"Description":[451,743,1101],"seqname":[452],"chr1":[453],"Chromosome":[454],"start":[455],"1782520":[456],"Start":[457],"position":[458,462],"end":[459],"1782770":[460],"End":[461],"mapq":[463],"60":[464],"Fragment":[465,602],"mapping":[466,472],"quality,":[467],"defined":[468],"minimum":[471],"quality":[473],"forward":[476],"reverse":[478],"strand":[480],"+":[481],"Strand":[482],"research":[489],"purposes":[490],"necessary,":[493],"tsv.gz":[495],"converted":[499],"format,":[502],"example":[504,1234],"when":[505],"an":[506,547,1106],"in-house":[507],"software":[508],"pipeline":[510],"only":[511],"accepts":[512],"input.":[515,755,766],"note":[517],"output":[520],"single-end":[523],"file,":[525,837],"each":[527,835,981,991,1046],"\u201cread\u201d":[528],"represents":[529],"cfDNA":[531],"fragment.":[532],"First,":[533],"convert":[534,556],"TSV":[536],"GRanges":[540,558],"object":[542,559,594,735,1074],"save":[544],"it":[545],".rds":[548],"file:":[549,994],"tsv_file=\"/path/to/tsv/file\"":[550],"Rscript":[551,565,862,939,1016],"--vanilla":[552,566,863,940],"./finaleDB/read_finaledb_frag_tsv_to_granges.r":[553],"${tsv_file}":[554],"Second,":[555],"format:":[562],"rds_file=\"/path/to/rds/file\"":[563],"output_dir=\"/path/to/output_dir/\"":[564],"./ulyses_scale_up_scripts/galp_to_bam.R":[567],"${rds_file}":[568],"${output_dir}":[569],"FALSE":[570],"3.":[571],"For":[577,834],"best":[578],"practices":[579],"science,":[582],"all":[583,617,713,1076],"features":[584,604,606,612,639,753,764,951],"stored":[590,884],"MultiAssayExperiment":[593,626,642,1073],"https://doi.org/10.5281/zenodo.18163904":[599],"These":[600,705],"include:":[601],"length":[603],"SD":[605],"C/T":[607],"ratio":[608,610],"S/L":[609],"CNA":[611],"Multidimensional":[613],"arrays":[614],"Metadata":[615],"are:":[622,1239],"MAE_object_for_cross_validation_samples.rds":[623],"MAE_object_for_heldout_test_samples.rds":[624],"MAE_object_for_unseen_test_samples.rds":[625],"structure":[630],"representing":[632],"analyzing":[634],"multi-omics":[635],"experiments.":[636],"To":[637],"extract":[638,950],"object,":[643],"please":[644],"refer":[645],"official":[648],"Bioconductor":[649],"documentation:":[650],"https://www.bioconductor.org/packages/release/bioc/vignettes/MultiAssayExperiment/inst/doc/MultiAssayExperiment.html":[651],"4.":[652],"Singularity,":[655],"version":[656,689],"singularity-ce":[657],"3.11.5-1.el8,":[658],"create":[662],"CNN":[664],"model":[665,761,772,788],"training":[666],"container":[667],"following":[670],"command:":[671],"singularity":[672],"pull":[673],"docker://pytorch/pytorch":[674],"obtained":[679],"Wednesday,":[681],"15":[682],"May":[683],"2024":[684],"at":[685,1178],"22:13:28":[686],"UTC.":[687],"number":[690,828],"22.04.":[692],"5.":[693],"locked":[697,709],"downloaded":[701],"https://doi.org/10.5281/zenodo.19150139":[704],"final":[708],"cross-validation":[714],"tested":[717],"unseen":[720],"samples.":[721],"A":[722],".pkl":[723],"Python":[726],"created":[730],"pickle,":[732],"Python\u2019s":[733],"built-in":[734],"serialization":[736],"module.":[737],"Model":[738,739],"File":[741],"size":[742],"UNITE-CNN":[744],"CNN.pkl":[745],"263":[746],"MB":[747,759,770],"ResNet18":[748],"architecture":[749],"C4":[751],"array":[752],"UNITE-XGB":[756],"XGB.pkl":[757],"2":[758,769],"XGBoost":[760,771],"X6":[763],"DELFI-XGB":[767],"DELFI.pkl":[768],"feature":[776],"set":[777],"DELFI":[780],"model.":[781,1172],"ichorCNA-TF":[782],"ichorCNA.pkl":[783],"19":[784],"KB":[785],"Logistic":[786],"regression":[787],"tumour":[790,1188],"fraction":[791,1189,1212],"inferred":[792,1213,1218,1223],"ichorCNA.":[794,1215,1220,1225],"6.":[795],"below":[803,986],"shows":[804],"how":[805],"run":[807],"Slurm":[814],"cluster.":[815],"6.1":[816],"Calculate":[817],"statistics":[819],"calculates":[822],"basic":[823],"statistics,":[825],"coverage.":[833],"corresponding":[839,988],"*.bam.summary.csv":[840,925],"will":[842,882],"generated.":[844,1051],"i":[846,923,996],"*.bam":[848],"do":[849,926,999],"sbatch":[850,927,1000,1062],"--time=0-10":[851],"--mem=128G":[852],"-J":[853,930,1006,1065],"\"count\"":[854],"\"epyc\"":[856,933],"--wrap=\"source":[857,934,1009],"~/.bashrc;":[858,935,1010],"R4_1;":[861,938,1014],"./ulyses_scale_up_scripts/summariseBam.R":[864],"${i}":[865,942],".":[866],"FALSE\"":[867],"done":[868,945,1031],"6.2":[869],"Downsample":[870],"target":[876],"depth":[877],"downsampled":[879,958],"downsampled_bam":[887],"folder.":[888],".bam.summary.csv":[890,915],"previous":[895,974],"input":[900],"step.":[903],"should":[907],"directory":[912,955,1054],"files.":[916,1259],"downsampled_dir=\"../downsampled_bam\"":[917],"target_depth=0.1":[918],"${downsampled_dir}":[921],"--time=0-20":[928],"--mem=32G":[929],"\"downsamp\"":[931],"./ulyses_scale_up_scripts/downsample_gatk.R":[941],"${target_depth}":[943],"${downsampled_dir}\"":[944],"6.3":[946],"Run":[947,962],"Set":[952],"working":[954],"containing":[956,1055],"files:":[960],"working_dir=\"./your_working_directory/\"":[961],"script:":[964],"./ulyses_scale_up_scripts/run_ulyses.sh":[966],"${working_dir}":[967],"6.4":[968],"Generate":[969],"plots":[971,989],"In":[972],"step,":[975],"*ulyses_image.rds":[976],"generates":[987],"RDS":[993],"*.ulyses_image.rds":[998],"--time=0-00:15:00":[1001],"\\":[1002,1005,1008,1011,1015,1018,1021,1024,1027],"--mem=1G":[1003],"--partition=epyc":[1004,1067],"\"plot\"":[1007],"./explore_packaged/functions/ulyses_image_to_features.R":[1017],"--image_file":[1019],"$i":[1020],"--specimen":[1022],"plasma":[1023,1152],"--isize_filter_min":[1025],"100":[1026],"--isize_filter_max":[1028],"220":[1029],"\"":[1030],"6.5":[1032],"Quality":[1033],"control":[1034],"results":[1037],"checks":[1040],"whether":[1041],"result":[1043,1058,1258],"sample":[1047],"have":[1048,1122],"been":[1049],"successfully":[1050],"Enter":[1052],"files,":[1059],"then":[1060],"--time=1-0":[1063],"--mem=8G":[1064],"QC":[1066],"--wrap=\"bash":[1068],"./ulyses_scale_up_scripts/QC_ulyses_results.sh\"":[1069],"6.6":[1070],"Build":[1071,1260],"Prepare":[1078],"CSV":[1080,1088],"metadata.":[1083,1235],"Each":[1084],"row":[1085],"corresponds":[1090],"one":[1092],"sample.":[1093],"described":[1098],"below.":[1099],"Variable":[1100],"cohort":[1102,1240],"name":[1104,1139],"abnormal":[1107],"condition":[1108],"healthy":[1110],"control.":[1111],"patient_id":[1112],"Individual":[1113],"identifier.":[1114],"specimen_id":[1115],"Specimen":[1116],"ID.":[1117],"patient":[1120],"multiple":[1123],"specimens.":[1124],"timepoint":[1125],"Time":[1126],"point":[1127],"specimen":[1129,1179],"collection.":[1130,1180],"bam_id":[1131,1241,1244],"name.":[1134],"study":[1135],"Study":[1136],"author":[1138],"dataset":[1142],"Fig.":[1144],"2A.":[1145],"sample_type":[1146],"Type":[1147],"body":[1149],"fluid.":[1150],"Only":[1151],"included":[1155],"study.":[1158],"stage":[1159],"Stage":[1160],"information.":[1161],"library_kit":[1162],"Library":[1163],"preparation":[1164],"kit.":[1165,1169],"extraction_kit":[1166],"DNA":[1167],"extraction":[1168],"seq_platform":[1170],"Sequencer":[1171],"age":[1173],"Age":[1174],"individual":[1177],"gender":[1181],"Sex":[1182,1222],"individual.":[1185],"clinical_tf":[1186],"Ground-truth":[1187],"reported":[1190],"publications.":[1192],"data_source":[1193],"Data":[1194],"origin.":[1195],"seq_depth":[1196],"Original":[1197],"haploid":[1198],"depth.":[1200],"mito_frac":[1201],"Fraction":[1202],"mitochondrial":[1204],"ichorcna_tf":[1210,1242],"Tumour":[1211],"ichorcna_ploidy":[1216],"Ploidy":[1217],"ichorcna_gender":[1221],"S2":[1229],"manuscript":[1232],"required":[1237],"fields":[1238],"field":[1245,1249],"key":[1248],"link":[1252],"MultiAssayExpe":[1262]},"counts_by_year":[],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2026-01-19T00:00:00"}
