{"id":"https://openalex.org/W7204568703","doi":"https://doi.org/10.64898/2026.08.25.747017","title":"CoTRA: a comprehensive R/Shiny framework for transparent bulk and single-cell RNA-seq analysis","display_name":"CoTRA: a comprehensive R/Shiny framework for transparent bulk and single-cell RNA-seq analysis","publication_year":2026,"publication_date":"2026-08-28","ids":{"openalex":"https://openalex.org/W7204568703","doi":"https://doi.org/10.64898/2026.08.25.747017"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.25.747017","doi":"https://doi.org/10.64898/2026.08.25.747017","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.25.747017","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/28/2026.08.25.747017.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/28/2026.08.25.747017.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070759140","display_name":"Umair Seemab","orcid":"https://orcid.org/0000-0002-4308-1109","observed_orcids":["https://orcid.org/0000-0002-4308-1109"]},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Umair Seemab","raw_affiliation_strings":["School of Pharmacy, University of Eastern Finland"],"raw_orcid":"https://orcid.org/0000-0002-4308-1109","affiliations":[{"raw_affiliation_string":"School of Pharmacy, University of Eastern Finland","institution_ids":["https://openalex.org/I175532246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094190842","display_name":"Katri Vainionp\u00e4\u00e4","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Katri Vainionpaa","raw_affiliation_strings":["School of Pharmacy, University of Eastern Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmacy, University of Eastern Finland","institution_ids":["https://openalex.org/I175532246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084617577","display_name":"Ziaurrehman Tanoli","orcid":"https://orcid.org/0000-0003-2435-9862","observed_orcids":["https://orcid.org/0000-0003-2435-9862"]},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I4210133586","display_name":"Institute for Molecular Medicine Finland","ror":"https://ror.org/030sbze61","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I4210133586"]},{"id":"https://openalex.org/I4391768107","display_name":"HiLIFE \u2013 El\u00e4m\u00e4ntieteiden Instituutti","ror":"https://ror.org/018bh0m68","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ziaurrehman Tanoli","raw_affiliation_strings":["Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4210133586","https://openalex.org/I4391768107"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035880873","display_name":"Henri Leinonen","orcid":"https://orcid.org/0000-0002-0388-832X","observed_orcids":["https://orcid.org/0000-0002-0388-832X"]},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Henri Leinonen","raw_affiliation_strings":["School of Pharmacy, University of Eastern Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmacy, University of Eastern Finland","institution_ids":["https://openalex.org/I175532246"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5070759140"],"corresponding_institution_ids":["https://openalex.org/I175532246"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9961000084877014,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9961000084877014,"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":0.001500000013038516,"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/T10885","display_name":"Gene expression and cancer classification","score":0.0008999999845400453,"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/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.8920000195503235},{"id":"https://openalex.org/keywords/bulk-rna-sequencing","display_name":"bulk RNA-seq","score":0.9980000257492065},{"id":"https://openalex.org/keywords/reproducible-analysis","display_name":"reproducible analysis","score":0.7670000195503235},{"id":"https://openalex.org/keywords/differential-gene-expression","display_name":"differential gene expression","score":0.7910000085830688},{"id":"https://openalex.org/keywords/cell-clustering","display_name":"cell clustering","score":0.6320000290870667},{"id":"https://openalex.org/keywords/cell-type-identification","display_name":"cell type annotation","score":0.8889999985694885},{"id":"https://openalex.org/keywords/single-cell-trajectory-inference","display_name":"single-cell trajectory analysis","score":0.7149999737739563},{"id":"https://openalex.org/keywords/intercellular-communication","display_name":"intercellular communication","score":0.8579999804496765},{"id":"https://openalex.org/keywords/pathway-activity","display_name":"pathway activity","score":0.8109999895095825},{"id":"https://openalex.org/keywords/differential-abundance-analysis","display_name":"differential abundance","score":0.847000002861023},{"id":"https://openalex.org/keywords/retinal-degeneration","display_name":"retinal degeneration","score":0.9490000009536743},{"id":"https://openalex.org/keywords/computational-performance","display_name":"computational performance","score":0.40700000524520874},{"id":"https://openalex.org/keywords/open-source-bioinformatics-software","display_name":"open-source bioinformatics software","score":0.6330000162124634},{"id":"https://openalex.org/keywords/deseq2","display_name":"DESeq2","score":0.6290000081062317},{"id":"https://openalex.org/keywords/seurat","display_name":"Seurat","score":0.8420000076293945},{"id":"https://openalex.org/keywords/edger","display_name":"edgeR","score":0.7170000076293945},{"id":"https://openalex.org/keywords/benchmarking","display_name":"benchmarking","score":0.40299999713897705}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7997000217437744},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.7414000034332275},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6437000036239624},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.5999000072479248},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.5681999921798706},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4487000107765198},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.4205000102519989},{"id":"https://openalex.org/C2780233690","wikidata":"https://www.wikidata.org/wiki/Q535347","display_name":"Transparency (behavior)","level":2,"score":0.41819998621940613},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.35659998655319214},{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.33739998936653137},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.33090001344680786},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.32710000872612},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.3158999979496002},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.3125},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.30649998784065247},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3012999892234802},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.2971000075340271},{"id":"https://openalex.org/C147494362","wikidata":"https://www.wikidata.org/wiki/Q2078905","display_name":"Troubleshooting","level":2,"score":0.29670000076293945},{"id":"https://openalex.org/C2780615140","wikidata":"https://www.wikidata.org/wiki/Q920419","display_name":"Upgrade","level":2,"score":0.2906999886035919},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.2856999933719635},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.28110000491142273},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.2806999981403351},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.2752000093460083},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.25940001010894775},{"id":"https://openalex.org/C20556612","wikidata":"https://www.wikidata.org/wiki/Q4469374","display_name":"Volume (thermodynamics)","level":2,"score":0.2533000111579895},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.25200000405311584},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.2513999938964844}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.25.747017","doi":"https://doi.org/10.64898/2026.08.25.747017","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.25.747017","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/28/2026.08.25.747017.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.25.747017","doi":"https://doi.org/10.64898/2026.08.25.747017","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.25.747017","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/28/2026.08.25.747017.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320316026","display_name":"Mary och Georg C. Ehrnrooths Stiftelse","ror":"https://ror.org/01ddjva78"},{"id":"https://openalex.org/F4320321726","display_name":"Suomen Kulttuurirahasto","ror":"https://ror.org/027xav248"},{"id":"https://openalex.org/F4320322456","display_name":"P\u00e4ivikki ja Sakari Sohlbergin S\u00e4\u00e4ti\u00f6","ror":"https://ror.org/03bj5da63"},{"id":"https://openalex.org/F4320322861","display_name":"Emil Aaltosen S\u00e4\u00e4ti\u00f6","ror":"https://ror.org/005rt3g54"},{"id":"https://openalex.org/F4320323760","display_name":"Sigrid Jus\u00e9liuksen S\u00e4\u00e4ti\u00f6","ror":"https://ror.org/00ckakm23"},{"id":"https://openalex.org/F4320324148","display_name":"Orionin Tutkimuss\u00e4\u00e4ti\u00f6","ror":"https://ror.org/0296s4x19"},{"id":"https://openalex.org/F4320327303","display_name":"De Blindas V\u00e4nner","ror":"https://ror.org/01nt19x17"},{"id":"https://openalex.org/F4320328031","display_name":"Silm\u00e4- ja kudospankkis\u00e4\u00e4ti\u00f6","ror":"https://ror.org/04y973974"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7204568703.pdf","grobid_xml":"https://content.openalex.org/works/W7204568703.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1968659469","https://openalex.org/W1981849943","https://openalex.org/W2036318837","https://openalex.org/W2069089843","https://openalex.org/W2114104545","https://openalex.org/W2149573463","https://openalex.org/W2154431984","https://openalex.org/W2159707944","https://openalex.org/W2179438025","https://openalex.org/W2190545194","https://openalex.org/W2236822143","https://openalex.org/W2429188508","https://openalex.org/W2572857085","https://openalex.org/W2739783898","https://openalex.org/W2742478344","https://openalex.org/W2746479894","https://openalex.org/W2800392236","https://openalex.org/W2898321887","https://openalex.org/W2903808414","https://openalex.org/W2907514116","https://openalex.org/W2916020270","https://openalex.org/W2919720720","https://openalex.org/W2949583997","https://openalex.org/W2951159620","https://openalex.org/W2951799803","https://openalex.org/W2980147288","https://openalex.org/W2989807288","https://openalex.org/W3005127469","https://openalex.org/W3044447231","https://openalex.org/W3132661792","https://openalex.org/W3174072032","https://openalex.org/W3175752499","https://openalex.org/W4225702304","https://openalex.org/W4226051960","https://openalex.org/W4233298626","https://openalex.org/W4313312743","https://openalex.org/W4380082653","https://openalex.org/W4388454971","https://openalex.org/W4400653746","https://openalex.org/W4417458297"],"related_works":["https://openalex.org/W7170049916","https://openalex.org/W7071356146","https://openalex.org/W2964277518","https://openalex.org/W3116514686","https://openalex.org/W4411852243","https://openalex.org/W4411572975","https://openalex.org/W4281295406","https://openalex.org/W4407098947","https://openalex.org/W3167078069","https://openalex.org/W7047841600"],"abstract_inverted_index":{"ABSTRACT":[0],"Bulk":[1],"RNA-seq":[2,5,41],"and":[3,22,33,50,81,101,108,115,124,140,168,173,179,218,249,265,267,286,307,311,346,356],"single-cell":[4,250,270],"(scRNA-seq)":[6],"are":[7,29],"widely":[8],"used":[9],"to":[10,31,148,212,227,239,328,333,354],"investigate":[11],"gene-expression":[12],"changes,":[13,260],"but":[14,205],"downstream":[15],"analysis":[16,352],"often":[17,209],"requires":[18,158,210],"multiple":[19],"statistical,":[20],"visualization,":[21],"reporting":[23,82],"tools,":[24],"creating":[25],"fragmented":[26],"workflows":[27,52,245,297],"that":[28,340],"difficult":[30],"configure":[32],"reproduce.":[34],"We":[35,224,272,338],"developed":[36,225],"CoTRA":[37,58,97,110,156,226,242,274,320],"(Comprehensive":[38],"Toolbox":[39],"for":[40,246],"Analysis),":[42],"an":[43],"open-source":[44],"R/Shiny":[45],"package":[46],"providing":[47],"independent":[48],"bulk":[49,121,248],"scRNA-seq":[51,125,145],"within":[53],"a":[54,334],"common":[55],"graphical":[56,244,296],"environment.":[57],"supports":[59],"quality":[60,255],"control,":[61],"differential":[62,73],"expression,":[63],"annotation,":[64,72,266],"enrichment,":[65],"dimensionality":[66],"reduction,":[67],"clustering,":[68],"marker":[69],"detection,":[70],"cell-type":[71],"abundance,":[74],"trajectory":[75],"inference,":[76],"pathway":[77],"activity,":[78],"cell-cell":[79],"communication,":[80],"while":[83,233],"exposing":[84],"key":[85],"analytical":[86,236],"parameters.":[87],"Compared":[88],"with":[89,151,282],"14":[90],"other":[91],"platforms":[92],"across":[93,199,358],"49":[94],"predefined":[95],"criteria,":[96],"fully":[98],"supported":[99,103],"46":[100],"partially":[102],"three.":[104],"Under":[105],"matched":[106],"inputs":[107],"parameters,":[109],"reproduced":[111,298],"direct":[112,283],"DESeq2,":[113],"edgeR,":[114],"Seurat":[116],"implementations,":[117],"including":[118],"identical":[119],"significant":[120],"gene":[122],"sets":[123],"clustering":[126,264],"(ARI":[127],"=":[128,131],"1.000;":[129],"NMI":[130],"1.000).":[132],"Retinal":[133],"case":[134],"studies":[135],"recapitulated":[136],"degeneration-associated":[137],"transcriptional":[138],"changes":[139],"demonstrated":[141],"cell-type-resolved":[142],"analysis.":[143],"Synthetic":[144],"benchmarking":[146],"scaled":[147],"50,000":[149],"cells":[150],"5.10":[152],"GB":[153],"peak":[154],"memory.":[155],"v1.0.0":[157],"R":[159],"\u2265":[160],"4.4.0,":[161],"has":[162],"been":[163],"tested":[164,273],"on":[165],"Linux,":[166],"Windows,":[167],"macOS,":[169],"is":[170,174,181],"GPL-3":[171],"licensed,":[172],"available":[175],"at":[176],"https://github.com/UmairSeemab/CoTRA":[177],",":[178],"support":[180],"provided":[182],"through":[183],"GitHub":[184],"Issues.":[185],"AUTHOR":[186],"SUMMARY":[187],"Modern":[188],"sequencing":[189],"technologies":[190],"can":[191],"measure":[192],"the":[193,240,299,304,312],"activity":[194],"of":[195,197,222,258,343],"thousands":[196],"genes":[198],"whole":[200],"tissues":[201],"or":[202],"individual":[203],"cells,":[204],"analyzing":[206],"these":[207],"data":[208,254,306,332],"researchers":[211,324],"combine":[213],"many":[214],"separate":[215],"software":[216],"tools":[217],"write":[219],"substantial":[220],"amounts":[221],"code.":[223],"make":[228,350],"this":[229,341],"process":[230],"more":[231],"accessible":[232],"keeping":[234],"important":[235],"choices":[237],"visible":[238],"user.":[241],"provides":[243],"both":[247],"RNA":[251],"sequencing,":[252],"covering":[253],"assessment,":[256],"identification":[257],"expression":[259,318,331],"biological":[261],"interpretation,":[262],"cell":[263],"several":[268],"advanced":[269],"analyses.":[271],"using":[275],"published":[276],"retinal":[277,313],"datasets,":[278],"compared":[279],"its":[280,288],"outputs":[281,348],"scripted":[284,301],"analyses,":[285],"measured":[287],"computational":[289],"performance":[290],"as":[291],"dataset":[292],"size":[293],"increased.":[294],"The":[295],"corresponding":[300],"results":[302],"when":[303],"same":[305],"parameters":[308],"were":[309],"used,":[310],"examples":[314],"recovered":[315],"expected":[316],"disease-associated":[317],"patterns.":[319],"runs":[321],"locally,":[322],"so":[323],"do":[325],"not":[326],"need":[327],"upload":[329],"their":[330],"mandatory":[335],"external":[336],"service.":[337],"hope":[339],"combination":[342],"accessibility,":[344],"transparency,":[345],"reproducible":[347],"will":[349],"transcriptomic":[351],"easier":[353],"use":[355],"inspect":[357],"collaborative":[359],"biomedical":[360],"research":[361],"projects.":[362]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-08-29T00:00:00"}
