{"id":"https://openalex.org/W4309247532","doi":"https://doi.org/10.1093/bioinformatics/btac746","title":"scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data","display_name":"scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data","publication_year":2022,"publication_date":"2022-11-17","ids":{"openalex":"https://openalex.org/W4309247532","doi":"https://doi.org/10.1093/bioinformatics/btac746","pmid":"https://pubmed.ncbi.nlm.nih.gov/36394263"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac746","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac746","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac746/48448680/btac746.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","license_id":"https://openalex.org/licenses/cc-by","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/39/1/btac746/48448680/btac746.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043484378","display_name":"Louis Faure","orcid":"https://orcid.org/0000-0003-4621-586X"},"institutions":[{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Louis Faure","raw_affiliation_strings":["Department of Neuroimmunology, Center for Brain Research, Medical University Vienna , 1090 Vienna, Austria"],"raw_orcid":"https://orcid.org/0000-0003-4621-586X","affiliations":[{"raw_affiliation_string":"Department of Neuroimmunology, Center for Brain Research, Medical University Vienna , 1090 Vienna, Austria","institution_ids":["https://openalex.org/I76134821"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060129715","display_name":"Ruslan Soldatov","orcid":"https://orcid.org/0000-0002-5670-5881"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruslan Soldatov","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034449272","display_name":"Peter V. Kharchenko","orcid":"https://orcid.org/0000-0002-6036-5875"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4387153853","display_name":"Altos Labs","ror":"https://ror.org/05467hx49","country_code":null,"type":"company","lineage":["https://openalex.org/I4387153853"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter V Kharchenko","raw_affiliation_strings":["Altos Labs , San Diego, CA 92121, USA","Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Altos Labs , San Diego, CA 92121, USA","institution_ids":["https://openalex.org/I4387153853"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076800395","display_name":"Igor Adameyko","orcid":"https://orcid.org/0000-0001-5471-0356"},"institutions":[{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Igor Adameyko","raw_affiliation_strings":["Department of Neuroimmunology, Center for Brain Research, Medical University Vienna , 1090 Vienna, Austria"],"raw_orcid":"https://orcid.org/0000-0001-5471-0356","affiliations":[{"raw_affiliation_string":"Department of Neuroimmunology, Center for Brain Research, Medical University Vienna , 1090 Vienna, Austria","institution_ids":["https://openalex.org/I76134821"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076800395"],"corresponding_institution_ids":["https://openalex.org/I76134821"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.363,"has_fulltext":true,"cited_by_count":105,"citation_normalized_percentile":{"value":0.9829101,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"39","issue":"1","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":0.9948999881744385,"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":0.9948999881744385,"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/T10604","display_name":"RNA Research and Splicing","score":0.0006000000284984708,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0006000000284984708,"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/python","display_name":"Python (programming language)","score":0.8603309988975525},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6988909244537354},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5380985140800476},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.4703431725502014},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.4501042068004608},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.42156368494033813},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.38327762484550476},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.355482280254364},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3291076123714447},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.13646262884140015}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8603309988975525},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6988909244537354},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5380985140800476},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.4703431725502014},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.4501042068004608},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.42156368494033813},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.38327762484550476},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.355482280254364},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3291076123714447},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.13646262884140015}],"mesh":[{"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":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac746","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac746","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac746/48448680/btac746.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36394263","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36394263","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:pubmedcentral.nih.gov:9805561","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9805561","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac746","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac746","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac746/48448680/btac746.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life below water","score":0.4699999988079071,"id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G1940342796","display_name":"Medical Neuroscience","funder_award_id":"DOC 33","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G5499129873","display_name":null,"funder_award_id":"33-B27","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G8793237861","display_name":null,"funder_award_id":"DOC 33-B27","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"}],"funders":[{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"},{"id":"https://openalex.org/F4320321491","display_name":"Cancerfonden","ror":"https://ror.org/0527jb766"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309247532.pdf","grobid_xml":"https://content.openalex.org/works/W4309247532.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W2107725277","https://openalex.org/W2108414494","https://openalex.org/W2587655168","https://openalex.org/W2800392236","https://openalex.org/W2916020270","https://openalex.org/W2925075625","https://openalex.org/W2941910667","https://openalex.org/W2948517648","https://openalex.org/W3009684066","https://openalex.org/W3081047001","https://openalex.org/W3087790240","https://openalex.org/W3143387950","https://openalex.org/W4205496949","https://openalex.org/W4214886807","https://openalex.org/W6761856697"],"related_works":["https://openalex.org/W4401016539","https://openalex.org/W4403672447","https://openalex.org/W1486009489","https://openalex.org/W4389426664","https://openalex.org/W3000262071","https://openalex.org/W3008797681","https://openalex.org/W4401878568","https://openalex.org/W4380871953","https://openalex.org/W4400651710","https://openalex.org/W2566205467"],"abstract_inverted_index":{"SUMMARY:":[0],"scFates":[1,65],"provides":[2],"an":[3],"extensive":[4],"toolset":[5],"for":[6,47],"the":[7,32,44,72,81],"analysis":[8,49],"of":[9,34,50,55],"dynamic":[10],"trajectories":[11,51],"comprising":[12],"tree":[13],"learning,":[14],"feature":[15],"association":[16],"testing,":[17],"branch":[18],"differential":[19],"expression":[20],"and":[21,28,60,77,98],"with":[22],"a":[23],"focus":[24],"on":[25,92,100,105],"cell":[26],"biasing":[27],"fate":[29],"splits":[30],"at":[31,85,94,107,115],"level":[33],"bifurcations.":[35],"It":[36],"is":[37,66,78,90],"meant":[38],"to":[39],"be":[40],"fully":[41],"integrated":[42],"into":[43],"scanpy":[45],"ecosystem":[46],"seamless":[48],"from":[52,80],"single-cell":[53],"data":[54,112],"various":[56],"modalities":[57],"(e.g.":[58],"RNA":[59],"ATAC).":[61],"AVAILABILITY":[62],"AND":[63],"IMPLEMENTATION:":[64],"released":[67],"as":[68],"open-source":[69],"software":[70],"under":[71],"BSD":[73],"3-Clause":[74],"'New'":[75],"License":[76],"available":[79,91,104,114],"Python":[82],"Package":[83],"Index":[84],"https://pypi.org/project/scFates/.":[86],"The":[87],"source":[88],"code":[89],"GitHub":[93,106],"https://github.com/LouisFaure/scFates/.":[95],"Code":[96],"reproduction":[97],"tutorials":[99],"published":[101],"datasets":[102],"are":[103,113],"https://github.com/LouisFaure/scFates_notebooks.":[108],"SUPPLEMENTARY":[109],"INFORMATION:":[110],"Supplementary":[111],"Bioinformatics":[116],"online.":[117]},"counts_by_year":[{"year":2026,"cited_by_count":20},{"year":2025,"cited_by_count":29},{"year":2024,"cited_by_count":38},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":4}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}
