{"id":"https://openalex.org/W3186843897","doi":"https://doi.org/10.1093/bioinformatics/btab549","title":"rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database","display_name":"rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database","publication_year":2021,"publication_date":"2021-07-26","ids":{"openalex":"https://openalex.org/W3186843897","doi":"https://doi.org/10.1093/bioinformatics/btab549","mag":"3186843897","pmid":"https://pubmed.ncbi.nlm.nih.gov/34320637"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab549","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab549","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/580/42039989/btab549.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/38/2/580/42039989/btab549.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053481898","display_name":"Daniel Osorio","orcid":"https://orcid.org/0000-0003-4424-8422"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Daniel Osorio","raw_affiliation_strings":["Centre for Molecular Medicine Norway (NCMM), University of Oslo , 0349 Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Molecular Medicine Norway (NCMM), University of Oslo , 0349 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081799863","display_name":"Marieke L. Kuijjer","orcid":"https://orcid.org/0000-0001-6280-3130"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]},{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]}],"countries":["NL","NO"],"is_corresponding":false,"raw_author_name":"Marieke L Kuijjer","raw_affiliation_strings":["Centre for Molecular Medicine Norway (NCMM), University of Oslo , 0349 Oslo, Norway","Department of Pathology, Leiden University Medical Center , Leiden, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0001-6280-3130","affiliations":[{"raw_affiliation_string":"Centre for Molecular Medicine Norway (NCMM), University of Oslo , 0349 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Pathology, Leiden University Medical Center , Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059360459","display_name":"James J. Cai","orcid":"https://orcid.org/0000-0002-8081-6725"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James J Cai","raw_affiliation_strings":["Center for Statistical Bioinformatics, Texas A&M University , College Station, TX 77843, USA","Department of Electrical & Computer Engineering, Texas A&M University , College Station, TX 77843, USA","Department of Veterinary Integrative Biosciences, Texas A&M University , College Station, TX 77843, USA","Interdisciplinary Program of Genetics, Texas A&M University , College Station, TX 77843, USA"],"raw_orcid":"https://orcid.org/0000-0002-8081-6725","affiliations":[{"raw_affiliation_string":"Center for Statistical Bioinformatics, Texas A&M University , College Station, TX 77843, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Department of Electrical & Computer Engineering, Texas A&M University , College Station, TX 77843, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Department of Veterinary Integrative Biosciences, Texas A&M University , College Station, TX 77843, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Interdisciplinary Program of Genetics, Texas A&M University , College Station, TX 77843, USA","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053481898"],"corresponding_institution_ids":["https://openalex.org/I184942183"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6663,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.66075275,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"2","first_page":"580","last_page":"582"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9977999925613403,"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":0.9977999925613403,"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/T11313","display_name":"Immune cells in cancer","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13410","display_name":"Immune responses and vaccinations","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.8560373783111572},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6633425354957581},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.5956799983978271},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5785230398178101},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.45046868920326233},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.43775543570518494},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.32677245140075684},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.23565560579299927},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.22653022408485413},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18020063638687134}],"concepts":[{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.8560373783111572},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6633425354957581},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.5956799983978271},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5785230398178101},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.45046868920326233},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.43775543570518494},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.32677245140075684},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.23565560579299927},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.22653022408485413},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18020063638687134}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btab549","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab549","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/580/42039989/btab549.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:34320637","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34320637","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:8723139","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8723139","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"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_3768804","is_oa":true,"landing_page_url":"https://academic.oup.com/bioinformatics/article/38/2/580/6329823","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"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":"Article / Letter to editor"},{"id":"pmh:oai:www.duo.uio.no:10852/90267","is_oa":true,"landing_page_url":"http://hdl.handle.net/10852/90267","pdf_url":null,"source":{"id":"https://openalex.org/S4306401716","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"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":"1367-4803","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab549","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab549","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/580/42039989/btab549.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":[{"id":"https://metadata.un.org/sdg/17","score":0.5099999904632568,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G6970925884","display_name":null,"funder_award_id":"187615","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8026655011","display_name":null,"funder_award_id":"187615","funder_id":"https://openalex.org/F4320323260","funder_display_name":"Universitetet i Oslo"},{"id":"https://openalex.org/G8437661840","display_name":"SCIENTIA-FELLOWS II: International Postdoctoral Fellowship Programme","funder_award_id":"801133","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323260","display_name":"Universitetet i Oslo","ror":"https://ror.org/01xtthb56"},{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3186843897.pdf","grobid_xml":"https://content.openalex.org/works/W3186843897.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1581614391","https://openalex.org/W1988201931","https://openalex.org/W2085581142","https://openalex.org/W2159707944","https://openalex.org/W2190545194","https://openalex.org/W2794480084","https://openalex.org/W2898701316","https://openalex.org/W2900981288","https://openalex.org/W2931036699","https://openalex.org/W2942880491","https://openalex.org/W2949177718","https://openalex.org/W2953067954","https://openalex.org/W2984472267","https://openalex.org/W3018809732","https://openalex.org/W3125797470","https://openalex.org/W3145969289"],"related_works":["https://openalex.org/W4389426664","https://openalex.org/W3008797681","https://openalex.org/W2566205467","https://openalex.org/W3012616639","https://openalex.org/W3126000805","https://openalex.org/W3198565742","https://openalex.org/W2010064959","https://openalex.org/W2157390150","https://openalex.org/W2119742499","https://openalex.org/W1985266044"],"abstract_inverted_index":{"MOTIVATION:":[0],"Characterizing":[1],"cells":[2,23,46,69],"with":[3,24,200],"rare":[4,126,150],"molecular":[5,27,73],"phenotypes":[6],"is":[7,33,222],"one":[8],"of":[9,12,52,67,80,122,144,160,167,183,211],"the":[10,25,44,65,71,77,81,106,115,120,157,163,171,180,184,187,191,209,212,230],"promises":[11],"high":[13],"throughput":[14],"single-cell":[15,55],"RNA":[16],"sequencing":[17],"(scRNA-seq)":[18],"techniques.":[19],"However,":[20],"collecting":[21,125,139],"enough":[22,68],"desired":[26,45,72,82],"phenotype":[28],"in":[29,203],"a":[30,59,88,136,142,149],"single":[31],"experiment":[32],"challenging,":[34],"requiring":[35],"several":[36],"samples":[37,194],"preprocessing":[38],"steps":[39],"to":[40,102],"filter":[41],"and":[42,104,109,140,162,195,206,215],"collect":[43],"experimentally":[47],"before":[48],"sequencing.":[49],"Data":[50],"integration":[51],"multiple":[53,131],"public":[54,132],"experiments":[56],"stands":[57],"as":[58,224],"solution":[60],"for":[61,124],"this":[62,85],"problem,":[63],"allowing":[64],"collection":[66],"exhibiting":[70],"signatures.":[74],"By":[75],"increasing":[76],"sample":[78],"size":[79],"cell":[83,90,127,152],"type,":[84,153],"approach":[86],"enables":[87],"robust":[89],"type":[91],"transcriptome":[92,175],"characterization.":[93],"RESULTS:":[94],"Here,":[95],"we":[96,134],"introduce":[97],"rPanglaoDB,":[98],"an":[99,225],"R":[100,226],"package":[101,227],"download":[103],"merge":[105],"uniformly":[107],"processed":[108],"annotated":[110],"scRNA-seq":[111],"data":[112],"provided":[113],"by":[114,129],"PanglaoDB":[116],"database.":[117],"To":[118],"show":[119],"potential":[121],"rPanglaoDB":[123,221],"types":[128],"integrating":[130],"datasets,":[133],"present":[135],"biological":[137],"application":[138],"characterizing":[141],"set":[143],"157":[145],"fibrocytes.":[146],"Fibrocytes":[147],"are":[148],"monocyte-derived":[151],"that":[154],"exhibits":[155],"both":[156],"inflammatory":[158],"features":[159],"macrophages":[161],"tissue":[164,193,204],"remodeling":[165],"properties":[166],"fibroblasts.":[168],"This":[169],"constitutes":[170],"first":[172],"fibrocytes'":[173],"unbiased":[174],"profile":[176,182],"report.":[177],"We":[178],"compared":[179],"transcriptomic":[181],"fibrocytes":[185],"against":[186],"fibroblasts":[188],"collected":[189],"from":[190],"same":[192],"confirm":[196],"their":[197],"associated":[198],"relationship":[199],"healing":[201],"processes":[202],"damage":[205],"infection":[207],"through":[208,229],"activation":[210],"prostaglandin":[213],"biosynthesis":[214],"regulation":[216],"pathway.":[217],"AVAILABILITY":[218],"AND":[219],"IMPLEMENTATION:":[220],"implemented":[223],"available":[228],"CRAN":[231],"repositories":[232],"https://CRAN.R-project.org/package=rPanglaoDB.":[233]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
