{"id":"https://openalex.org/W2161643019","doi":"https://doi.org/10.1093/bioinformatics/btt351","title":"CellMix: a comprehensive toolbox for gene expression deconvolution","display_name":"CellMix: a comprehensive toolbox for gene expression deconvolution","publication_year":2013,"publication_date":"2013-07-03","ids":{"openalex":"https://openalex.org/W2161643019","doi":"https://doi.org/10.1093/bioinformatics/btt351","mag":"2161643019","pmid":"https://pubmed.ncbi.nlm.nih.gov/23825367"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt351","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt351","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084757561","display_name":"Renaud Gaujoux","orcid":null},"institutions":[{"id":"https://openalex.org/I157614274","display_name":"University of Cape Town","ror":"https://ror.org/03p74gp79","country_code":"ZA","type":"education","lineage":["https://openalex.org/I157614274"]},{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE","ZA"],"is_corresponding":true,"raw_author_name":"Renaud Gaujoux","raw_affiliation_strings":["1 Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa and 2School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa and 2School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Ireland","institution_ids":["https://openalex.org/I188760350","https://openalex.org/I157614274"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004762593","display_name":"Cathal Seoighe","orcid":"https://orcid.org/0000-0003-0496-4029"},"institutions":[{"id":"https://openalex.org/I157614274","display_name":"University of Cape Town","ror":"https://ror.org/03p74gp79","country_code":"ZA","type":"education","lineage":["https://openalex.org/I157614274"]},{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE","ZA"],"is_corresponding":false,"raw_author_name":"Cathal Seoighe","raw_affiliation_strings":["1 Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa and 2School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa and 2School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Ireland","institution_ids":["https://openalex.org/I188760350","https://openalex.org/I157614274"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5084757561"],"corresponding_institution_ids":["https://openalex.org/I157614274","https://openalex.org/I188760350"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":7.6272,"has_fulltext":false,"cited_by_count":210,"citation_normalized_percentile":{"value":0.98098359,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"29","issue":"17","first_page":"2211","last_page":"2212"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.7281000018119812,"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":0.7281000018119812,"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":0.2013999968767166,"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":0.01489999983459711,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.9612067937850952},{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.8517880439758301},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.648156464099884},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6272236704826355},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5093423128128052},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.466054767370224},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4641175866127014},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4581422507762909},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4365052282810211},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3280155062675476},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27677321434020996},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.18176066875457764},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13447561860084534},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07427605986595154}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9612067937850952},{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.8517880439758301},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.648156464099884},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6272236704826355},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5093423128128052},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.466054767370224},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4641175866127014},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4581422507762909},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4365052282810211},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3280155062675476},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27677321434020996},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.18176066875457764},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13447561860084534},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07427605986595154}],"mesh":[{"descriptor_ui":"D002461","descriptor_name":"Cell Line, Transformed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002461","descriptor_name":"Cell Line, Transformed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002461","descriptor_name":"Cell Line, Transformed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt351","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt351","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23825367","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23825367","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:http://www.rian.ie/160618/","is_oa":false,"landing_page_url":"http://hdl.handle.net/10379/11597","pdf_url":null,"source":{"id":"https://openalex.org/S4306400033","display_name":"Arrow@dit (Dublin Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I115570527","host_organization_name":"Dublin Institute of Technology","host_organization_lineage":["https://openalex.org/I115570527"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2028426093","https://openalex.org/W2030781210","https://openalex.org/W2033642329","https://openalex.org/W2093358653","https://openalex.org/W2129271267","https://openalex.org/W2129631522","https://openalex.org/W2140802251","https://openalex.org/W2149031002","https://openalex.org/W2155388222","https://openalex.org/W2160697532","https://openalex.org/W2607741101"],"related_works":["https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W2140163842","https://openalex.org/W3156537409","https://openalex.org/W2747931568","https://openalex.org/W2921090651","https://openalex.org/W2133055377","https://openalex.org/W2287365612"],"abstract_inverted_index":{"UNLABELLED:":[0],"Gene":[1],"expression":[2,41,67,131],"data":[3,132],"are":[4,12],"typically":[5],"generated":[6],"from":[7,133,148],"heterogeneous":[8,134],"biological":[9,87],"samples":[10],"that":[11,108],"composed":[13],"of":[14,49,59,64,84,99],"multiple":[15],"cell":[16],"or":[17,55],"tissue":[18],"types,":[19],"in":[20,35,45],"varying":[21],"proportions,":[22],"each":[23],"contributing":[24],"to":[25,72,125,155],"global":[26,65],"gene":[27,66,130],"expression.":[28],"This":[29],"heterogeneity":[30],"is":[31,68,146,151],"a":[32,80,121],"major":[33],"confounder":[34],"standard":[36],"analysis":[37,83],"such":[38,100],"as":[39],"differential":[40],"analysis,":[42],"where":[43],"differences":[44],"the":[46,50,57,85,90,97],"relative":[47],"proportions":[48],"constituent":[51],"cells":[52],"may":[53],"prevent":[54],"bias":[56],"detection":[58],"cell-specific":[60],"differences.":[61],"Computational":[62],"deconvolution":[63,112],"an":[69,105,115],"appealing":[70],"alternative":[71],"costly":[73],"physical":[74],"sample":[75],"separation":[76],"techniques":[77],"and":[78,95,117,128,145,165],"enables":[79],"more":[81],"detailed":[82],"underlying":[86],"processes":[88],"at":[89],"cell-type":[91],"level.":[92],"To":[93],"facilitate":[94],"popularize":[96],"application":[98],"methods,":[101,113],"we":[102],"developed":[103],"CellMix,":[104],"R":[106],"package":[107,141],"incorporates":[109],"most":[110],"state-of-the-art":[111],"into":[114],"intuitive":[116],"extendible":[118],"framework,":[119],"providing":[120],"single":[122],"entry":[123],"point":[124],"explore,":[126],"assess":[127],"disentangle":[129],"samples.":[135],"AVAILABILITY":[136],"AND":[137],"IMPLEMENTATION:":[138],"The":[139,157],"CellMix":[140],"builds":[142],"on":[143],"R/BioConductor":[144],"available":[147],"http://web.cbio.uct.ac.za/\u223crenaud/CRAN/web/CellMix.":[149],"It":[150],"currently":[152],"being":[153],"submitted":[154],"BioConductor.":[156],"package's":[158],"vignettes":[159],"notably":[160],"contain":[161],"additional":[162],"information,":[163],"examples":[164],"references.":[166]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":20},{"year":2019,"cited_by_count":23},{"year":2018,"cited_by_count":33},{"year":2017,"cited_by_count":21},{"year":2016,"cited_by_count":32},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
