{"id":"https://openalex.org/W2954504102","doi":"https://doi.org/10.1093/bioinformatics/btz348","title":"scOrange\u2014a tool for hands-on training of concepts from single-cell data analytics","display_name":"scOrange\u2014a tool for hands-on training of concepts from single-cell data analytics","publication_year":2019,"publication_date":"2019-05-10","ids":{"openalex":"https://openalex.org/W2954504102","doi":"https://doi.org/10.1093/bioinformatics/btz348","mag":"2954504102","pmid":"https://pubmed.ncbi.nlm.nih.gov/31510695"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz348","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz348","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i4/28913840/btz348.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i4/28913840/btz348.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054448749","display_name":"Martin Stra\u017ear","orcid":"https://orcid.org/0000-0003-3064-1055"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Martin Stra\u017ear","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033376376","display_name":"Lan \u017dagar","orcid":null},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Lan \u017dagar","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041220000","display_name":"Jaka Koko\u0161ar","orcid":"https://orcid.org/0000-0001-7834-4573"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Jaka Koko\u0161ar","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066265122","display_name":"Vesna Tanko","orcid":null},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Vesna Tanko","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035860722","display_name":"Ale\u0161 Erjavec","orcid":null},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Ale\u0161 Erjavec","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054118774","display_name":"Pavlin G. Poli\u010dar","orcid":"https://orcid.org/0000-0002-6462-9372"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Pavlin G Poli\u010dar","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056539596","display_name":"An\u017ee Stari\u010d","orcid":null},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"An\u017ee Stari\u010d","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024075429","display_name":"Janez Dem\u0161ar","orcid":"https://orcid.org/0000-0002-1256-1687"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Janez Dem\u0161ar","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055034051","display_name":"Gad Shaulsky","orcid":"https://orcid.org/0000-0002-0532-0551"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gad Shaulsky","raw_affiliation_strings":["Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013606443","display_name":"Vilas Menon","orcid":"https://orcid.org/0000-0002-4096-8601"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vilas Menon","raw_affiliation_strings":["Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069615450","display_name":"Andrew L. Lemire","orcid":"https://orcid.org/0000-0002-0624-3789"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I195573530","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Lemire","raw_affiliation_strings":["Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I195573530"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049866282","display_name":"Anup Parikh","orcid":"https://orcid.org/0000-0003-3120-1721"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Anup Parikh","raw_affiliation_strings":["Naringi, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Naringi, San Francisco, CA, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073792028","display_name":"Bla\u017e Zupan","orcid":"https://orcid.org/0000-0002-5864-7056"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["SI","US"],"is_corresponding":true,"raw_author_name":"Bla\u017e Zupan","raw_affiliation_strings":["Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA","Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5073792028"],"corresponding_institution_ids":["https://openalex.org/I153976015","https://openalex.org/I181547552"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6826,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.67230469,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"35","issue":"14","first_page":"i4","last_page":"i12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9943000078201294,"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":0.9943000078201294,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0017000000225380063,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.00039999998989515007,"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/analytics","display_name":"Analytics","score":0.7330284118652344},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7222630977630615},{"id":"https://openalex.org/keywords/training","display_name":"Training (meteorology)","score":0.6943925023078918},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5531901717185974},{"id":"https://openalex.org/keywords/data-analysis","display_name":"Data analysis","score":0.49773910641670227},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.49099448323249817},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.47200772166252136},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32113951444625854},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2957971692085266},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2893517017364502},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11555212736129761}],"concepts":[{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.7330284118652344},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7222630977630615},{"id":"https://openalex.org/C2777211547","wikidata":"https://www.wikidata.org/wiki/Q17141490","display_name":"Training (meteorology)","level":2,"score":0.6943925023078918},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5531901717185974},{"id":"https://openalex.org/C175801342","wikidata":"https://www.wikidata.org/wiki/Q1988917","display_name":"Data analysis","level":2,"score":0.49773910641670227},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.49099448323249817},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.47200772166252136},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32113951444625854},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2957971692085266},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2893517017364502},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11555212736129761},{"id":"https://openalex.org/C153294291","wikidata":"https://www.wikidata.org/wiki/Q25261","display_name":"Meteorology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz348","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz348","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i4/28913840/btz348.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31510695","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31510695","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:5588676","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6612816","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz348","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz348","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i4/28913840/btz348.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.41999998688697815}],"awards":[{"id":"https://openalex.org/G1574574160","display_name":null,"funder_award_id":"R35 GM118016","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5769677123","display_name":"Artificial Intelligence and Intelligent Systems","funder_award_id":"P2-0209","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G7323532721","display_name":null,"funder_award_id":"Program Grant P2-0209","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"}],"funders":[{"id":"https://openalex.org/F2519919948","display_name":"Janelia Research Campus","ror":"https://ror.org/013sk6x84"},{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2954504102.pdf","grobid_xml":"https://content.openalex.org/works/W2954504102.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1629043538","https://openalex.org/W1779656687","https://openalex.org/W2010653277","https://openalex.org/W2013434113","https://openalex.org/W2022406334","https://openalex.org/W2045317504","https://openalex.org/W2069089843","https://openalex.org/W2096525273","https://openalex.org/W2102212449","https://openalex.org/W2102794349","https://openalex.org/W2103017472","https://openalex.org/W2131681506","https://openalex.org/W2131850886","https://openalex.org/W2143476736","https://openalex.org/W2163805179","https://openalex.org/W2302501749","https://openalex.org/W2465917013","https://openalex.org/W2583408446","https://openalex.org/W2620827867","https://openalex.org/W2680916460","https://openalex.org/W2773787581","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2951506174","https://openalex.org/W3099768174","https://openalex.org/W4251386234"],"related_works":["https://openalex.org/W4394050964","https://openalex.org/W4226266853","https://openalex.org/W4210252074","https://openalex.org/W3092201768","https://openalex.org/W2796632413","https://openalex.org/W2551249631","https://openalex.org/W2740083192","https://openalex.org/W2794907032","https://openalex.org/W4255802207","https://openalex.org/W4299701476"],"abstract_inverted_index":{"MOTIVATION:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"allows":[4],"us":[5],"to":[6,16,57,153],"simultaneously":[7],"profile":[8],"the":[9,69,72,75,151,158,164,168,180,195],"transcriptomes":[10],"of":[11,13,25,30,36,68,71,111,167,186,212],"thousands":[12],"cells":[14],"and":[15,23,44,54,59,74,97,123,142,175,208],"indulge":[17],"in":[18,50,85,146,157],"exploring":[19],"cell":[20],"diversity,":[21],"development":[22],"discovery":[24],"new":[26],"molecular":[27,48],"mechanisms.":[28],"Analysis":[29],"scRNA":[31],"data":[32,41,52,62,87,94,113,187],"involves":[33],"a":[34,82,98,107,112,177],"combination":[35],"non-trivial":[37],"steps":[38],"from":[39],"statistics,":[40],"visualization,":[42],"bioinformatics":[43],"machine":[45],"learning.":[46],"Training":[47],"biologists":[49],"single-cell":[51,86],"analysis":[53,95,143,188],"empowering":[55],"them":[56],"review":[58,163],"analyze":[60],"their":[61],"can":[63,129,192],"be":[64],"challenging,":[65],"both":[66],"because":[67],"complexity":[70],"methods":[73,136],"steep":[76],"learning":[77],"curve.":[78],"RESULTS:":[79],"We":[80,161,182],"propose":[81,176],"workshop-style":[83],"training":[84,103,135],"analytics":[88],"that":[89,116,137,171,190],"relies":[90,104],"on":[91,105,139],"an":[92,202,209],"explorative":[93],"toolbox":[96,170],"hands-on":[99],"teaching":[100],"style.":[101],"The":[102,205],"scOrange,":[106],"newly":[108],"developed":[109],"extension":[110],"mining":[114],"framework":[115],"features":[117],"workflow":[118],"design":[119,165],"through":[120,144],"visual":[121],"programming":[122,141],"interactive":[124],"visualizations.":[125],"Workshops":[126],"with":[127],"scOrange":[128,169,200],"proceed":[130],"much":[131],"faster":[132],"than":[133],"similar":[134],"rely":[138],"computer":[140],"scripting":[145],"R":[147],"or":[148],"Python,":[149],"allowing":[150],"trainer":[152],"cover":[154],"more":[155],"ground":[156],"same":[159],"time-frame.":[160],"here":[162],"principles":[166],"support":[172],"such":[173],"workshops":[174],"syllabus":[178],"for":[179],"course.":[181],"also":[183],"provide":[184],"examples":[185],"workflows":[189],"instructors":[191],"use":[193],"during":[194],"training.":[196],"AVAILABILITY":[197],"AND":[198],"IMPLEMENTATION:":[199],"is":[201],"open-source":[203],"software.":[204],"software,":[206],"documentation":[207],"emerging":[210],"set":[211],"educational":[213],"videos":[214],"are":[215],"available":[216],"at":[217],"http://singlecell.biolab.si.":[218]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}