{"id":"https://openalex.org/W4399521663","doi":"https://doi.org/10.32614/cran.package.sctenifoldknk","title":"scTenifoldKnk: In-Silico Knockout Experiments from Single-Cell Gene Regulatory Networks","display_name":"scTenifoldKnk: In-Silico Knockout Experiments from Single-Cell Gene Regulatory Networks","publication_year":2020,"publication_date":"2020-11-23","ids":{"openalex":"https://openalex.org/W4399521663","doi":"https://doi.org/10.32614/cran.package.sctenifoldknk"},"language":"en","primary_location":{"id":"doi:10.32614/cran.package.sctenifoldknk","doi":"https://doi.org/10.32614/cran.package.sctenifoldknk","is_oa":true,"landing_page_url":"http://dx.doi.org/10.32614/cran.package.sctenifoldknk","pdf_url":"https://cran.r-project.org/web/packages/scTenifoldKnk/scTenifoldKnk.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"CRAN: Contributed Packages","raw_type":"dataset"},"volume":null,"type":"dataset","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://cran.r-project.org/web/packages/scTenifoldKnk/scTenifoldKnk.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053481898","display_name":"Daniel Osorio","orcid":"https://orcid.org/0000-0003-4424-8422","observed_orcids":["https://orcid.org/0000-0003-4424-8422"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel Osorio","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-4424-8422","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066519862","display_name":"Yan Zhong","orcid":"https://orcid.org/0000-0003-2412-043X","observed_orcids":["https://orcid.org/0000-0003-2412-043X"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yan Zhong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052075967","display_name":"Guanxun Li","orcid":"https://orcid.org/0000-0002-2449-4469","observed_orcids":["https://orcid.org/0000-0002-2449-4469"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Guanxun Li","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101701152","display_name":"Qian Xu","orcid":"https://orcid.org/0000-0001-9521-7912","observed_orcids":["https://orcid.org/0000-0001-9521-7912"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qian Xu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143320732","display_name":"Yongjuan Yang","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yongjian Yang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102993900","display_name":"Yanan Tian","orcid":"https://orcid.org/0000-0002-3543-9529","observed_orcids":["https://orcid.org/0000-0002-3543-9529"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yanan Tian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019568866","display_name":"Robert S. Chapkin","orcid":"https://orcid.org/0000-0002-6515-3898","observed_orcids":["https://orcid.org/0000-0002-6515-3898"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robert Chapkin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091595137","display_name":"Jianhua Huang","orcid":"https://orcid.org/0000-0001-6509-1765","observed_orcids":["https://orcid.org/0000-0001-6509-1765","https://orcid.org/0000-0001-8506-8255"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jianhua Huang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5059360459","display_name":"James J. Cai","orcid":"https://orcid.org/0000-0002-8081-6725","observed_orcids":["https://orcid.org/0000-0002-8081-6725"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"James J. Cai","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-8081-6725","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9794999957084656,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9794999957084656,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.018200000748038292,"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/T10887","display_name":"Bioinformatics and Genomic Networks","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/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.8349999785423279},{"id":"https://openalex.org/keywords/gene-function-prediction","display_name":"gene function prediction","score":0.49000000953674316},{"id":"https://openalex.org/keywords/network-perturbation","display_name":"network perturbation","score":0.5879999995231628},{"id":"https://openalex.org/keywords/differential-gene-regulation","display_name":"differential gene regulation","score":0.550000011920929}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8789325952529907},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6122763752937317},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6001904010772705},{"id":"https://openalex.org/C77957584","wikidata":"https://www.wikidata.org/wiki/Q1133550","display_name":"Gene knockout","level":3,"score":0.4841935932636261},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45647579431533813},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.44735607504844666},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44112628698349},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.4269734025001526},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.21346232295036316}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.32614/cran.package.sctenifoldknk","doi":"https://doi.org/10.32614/cran.package.sctenifoldknk","is_oa":true,"landing_page_url":"http://dx.doi.org/10.32614/cran.package.sctenifoldknk","pdf_url":"https://cran.r-project.org/web/packages/scTenifoldKnk/scTenifoldKnk.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"CRAN: Contributed Packages","raw_type":"dataset"}],"best_oa_location":{"id":"doi:10.32614/cran.package.sctenifoldknk","doi":"https://doi.org/10.32614/cran.package.sctenifoldknk","is_oa":true,"landing_page_url":"http://dx.doi.org/10.32614/cran.package.sctenifoldknk","pdf_url":"https://cran.r-project.org/web/packages/scTenifoldKnk/scTenifoldKnk.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"CRAN: Contributed Packages","raw_type":"dataset"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4399521663.pdf","grobid_xml":"https://content.openalex.org/works/W4399521663.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2003194288","https://openalex.org/W2513589746","https://openalex.org/W2153919606","https://openalex.org/W2213189664","https://openalex.org/W2074002899","https://openalex.org/W2062254828","https://openalex.org/W4237480606","https://openalex.org/W2936968863","https://openalex.org/W2941821699","https://openalex.org/W1971792277"],"abstract_inverted_index":{"A":[0],"workflow":[1],"based":[2],"on":[3],"'scTenifoldNet'":[4],"to":[5,53,66,78],"perform":[6],"in-silico":[7],"knockout":[8,85],"experiments":[9],"using":[10],"single-cell":[11,28],"RNA":[12],"sequencing":[13],"(scRNA-seq)":[14],"data":[15],"from":[16,39],"wild-type":[17],"(WT)":[18],"control":[19],"samples":[20],"as":[21],"input.":[22],"First,":[23],"the":[24,40,44,49,58,63,80,83,88,92],"package":[25],"constructs":[26],"a":[27,36],"gene":[29,38,84],"regulatory":[30],"network":[31],"(scGRN)":[32],"and":[33,86],"knocks":[34],"out":[35,60],"target":[37],"adjacency":[41],"matrix":[42],"of":[43,82],"WT":[45,64],"scGRN":[46,61,65],"by":[47],"setting":[48],"gene\u2019s":[50,89],"outdegree":[51],"edges":[52],"zero.":[54],"Then,":[55],"it":[56],"compares":[57],"knocked":[59],"with":[62],"identify":[67],"differentially":[68],"regulated":[69],"genes,":[70,74],"called":[71],"virtual-knockout":[72],"perturbed":[73],"which":[75],"are":[76],"used":[77],"assess":[79],"impact":[81],"reveal":[87],"function":[90],"in":[91],"analyzed":[93],"cells.":[94]},"counts_by_year":[],"updated_date":"2026-09-24T07:57:37.273135","created_date":"2025-10-10T00:00:00"}
