{"id":"https://openalex.org/W6931309350","doi":"https://doi.org/10.5281/zenodo.8014246","title":"singleCellTK v2.8.1","display_name":"singleCellTK v2.8.1","publication_year":2023,"publication_date":"2023-06-07","ids":{"openalex":"https://openalex.org/W6931309350","doi":"https://doi.org/10.5281/zenodo.8014246"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:8014246","is_oa":true,"landing_page_url":"https://zenodo.org/record/8014246","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"software"},"type":"software","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/8014246","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Wang, Yichen","orcid":"https://orcid.org/0000-0003-4347-5199"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wang, Yichen","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":"https://orcid.org/0000-0003-4347-5199","affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sarfraz, Irzam","orcid":"https://orcid.org/0000-0001-8121-792X"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarfraz, Irzam","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":"https://orcid.org/0000-0001-8121-792X","affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Pervaiz, Nida","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pervaiz, Nida","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hong, Rui","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong, Rui","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Koga, Yusuke","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Koga, Yusuke","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Akavoor, Vidya","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Akavoor, Vidya","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Xinyun Cao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xinyun Cao","raw_affiliation_strings":["Software & Application Innovation Lab, Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Software & Application Innovation Lab, Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston, MA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Alabdullatif, Salam","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alabdullatif, Salam","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zaib, Syed Ali","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zaib, Syed Ali","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Wang, Zhe","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wang, Zhe","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jansen, Frederick","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jansen, Frederick","raw_affiliation_strings":["Software & Application Innovation Lab, Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Software & Application Innovation Lab, Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston, MA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yajima, Masanao","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yajima, Masanao","raw_affiliation_strings":["Department of Mathematics and Statistics, Boston University, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, Boston University, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"W. Evan Johnson","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. Evan Johnson","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","author":{"id":null,"display_name":"Campbell, Joshua D.","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Campbell, Joshua D.","raw_affiliation_strings":["Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"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":true,"primary_topic":{"id":"https://openalex.org/T10410","display_name":"COVID-19 epidemiological studies","score":0.24220000207424164,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10410","display_name":"COVID-19 epidemiological studies","score":0.24220000207424164,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11296","display_name":"COVID-19 and healthcare impacts","score":0.1535000056028366,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T13398","display_name":"Data Analysis with R","score":0.023000000044703484,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/workflow","display_name":"Workflow","score":0.8363000154495239},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6504999995231628},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.6316999793052673},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5968999862670898},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5041999816894531},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.4690000116825104}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8363000154495239},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7523999810218811},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6504999995231628},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.6316999793052673},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5968999862670898},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5041999816894531},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.4690000116825104},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4397999942302704},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.3481000065803528},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.3368000090122223},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33219999074935913},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.28380000591278076},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.26739999651908875},{"id":"https://openalex.org/C198352243","wikidata":"https://www.wikidata.org/wiki/Q37105","display_name":"Line (geometry)","level":2,"score":0.257099986076355},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.2565000057220459},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.2535000145435333},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.25270000100135803}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:8014246","is_oa":true,"landing_page_url":"https://zenodo.org/record/8014246","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"software"},{"id":"doi:10.5281/zenodo.8014246","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.8014246","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":"pmh:oai:zenodo.org:8014246","is_oa":true,"landing_page_url":"https://zenodo.org/record/8014246","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"software"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"The":[0],"Single":[1],"Cell":[2],"Toolkit":[3],"(SCTK)":[4],"in":[5,127],"the":[6,41,52,113,117,128],"singleCellTK":[7],"package":[8],"provides":[9],"an":[10,134],"interface":[11],"to":[12,30,55,101],"popular":[13],"tools":[14,33],"for":[15,58],"importing,":[16,60],"quality":[17,107],"control,":[18],"analysis,":[19,92],"and":[20,71,93,104,149,160],"visualization":[21],"of":[22,40,62],"single":[23],"cell":[24,88],"RNA-seq":[25],"data.":[26],"SCTK":[27],"allows":[28],"users":[29,51],"seamlessly":[31],"integrate":[32],"from":[34],"various":[35],"packages":[36],"at":[37,165],"different":[38],"stages":[39],"analysis":[42],"workflow.":[43],"A":[44],"general":[45,63],"\"a":[46],"la":[47],"carte\"":[48],"workflow":[49],"gives":[50],"ability":[53],"access":[54],"multiple":[56],"methods":[57],"data":[59,94,124],"calculation":[61],"QC":[64],"metrics,":[65],"doublet":[66],"detection,":[67,85],"ambient":[68],"RNA":[69],"estimation":[70],"removal,":[72],"filtering,":[73],"normalization,":[74],"batch":[75],"correction":[76],"or":[77,131,143],"integration,":[78],"dimensionality":[79],"reduction,":[80],"2-D":[81],"embedding,":[82],"clustering,":[83],"marker":[84],"differential":[86],"expression,":[87],"type":[89],"labeling,":[90],"pathway":[91],"exporting.":[95],"Curated":[96],"workflows":[97,145],"can":[98,109,121,146,162],"be":[99,110,147,163],"used":[100],"run":[102],"Seurat":[103],"Celda.":[105],"Streamlined":[106],"control":[108],"performed":[111],"on":[112],"command":[114],"line":[115],"using":[116,125,133],"SCTK-QC":[118],"pipeline.":[119],"Users":[120],"analyze":[122],"their":[123],"commands":[126],"R":[129],"console":[130],"by":[132,156],"interactive":[135],"Shiny":[136],"Graphical":[137],"User":[138],"Interface":[139],"(GUI).":[140],"Specific":[141],"analyses":[142],"entire":[144],"summarized":[148],"shared":[150],"with":[151],"comprehensive":[152],"HTML":[153],"reports":[154],"generated":[155],"Rmarkdown.":[157],"Additional":[158],"documentation":[159],"vignettes":[161],"found":[164],"camplab.net/sctk.<br>":[166]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2025-10-10T00:00:00"}
