{"id":"https://openalex.org/W7140923077","doi":"https://doi.org/10.1093/bioinformatics/btag151","title":"phylobar: an R package for multiresolution compositional barplots in omics studies","display_name":"phylobar: an R package for multiresolution compositional barplots in omics studies","publication_year":2026,"publication_date":"2026-03-24","ids":{"openalex":"https://openalex.org/W7140923077","doi":"https://doi.org/10.1093/bioinformatics/btag151","pmid":"https://pubmed.ncbi.nlm.nih.gov/41883130"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag151","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag151","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag151","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109421846","display_name":"M. Tien Kuo","orcid":null},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Megan Kuo","raw_affiliation_strings":["University of Wisconsin-Madison Department of Statistics, , Madison, WI 53703,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Wisconsin-Madison Department of Statistics, , Madison, WI 53703,","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091163780","display_name":"Kim\u2010Anh L\u00ea Cao","orcid":"https://orcid.org/0000-0003-3923-1116"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210166212","display_name":"Melbourne Genomics Health Alliance","ror":"https://ror.org/05rwzhy90","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I4210166212"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Kim-Anh L\u00ea Cao","raw_affiliation_strings":["University of Melbourne Melbourne Integrative Genomics, School of Mathematics and Statistics, , Melbourne, VIC 3052,"],"raw_orcid":"https://orcid.org/0000-0003-3923-1116","affiliations":[{"raw_affiliation_string":"University of Melbourne Melbourne Integrative Genomics, School of Mathematics and Statistics, , Melbourne, VIC 3052,","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210166212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086699730","display_name":"Saritha Kodikara","orcid":"https://orcid.org/0000-0002-7039-8398"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210166212","display_name":"Melbourne Genomics Health Alliance","ror":"https://ror.org/05rwzhy90","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I4210166212"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Saritha Kodikara","raw_affiliation_strings":["University of Melbourne Melbourne Integrative Genomics, School of Mathematics and Statistics, , Melbourne, VIC 3052,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Melbourne Melbourne Integrative Genomics, School of Mathematics and Statistics, , Melbourne, VIC 3052,","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210166212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065359043","display_name":"Jiadong Mao","orcid":"https://orcid.org/0000-0002-3818-1981"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210166212","display_name":"Melbourne Genomics Health Alliance","ror":"https://ror.org/05rwzhy90","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I4210166212"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Jiadong Mao","raw_affiliation_strings":["University of Melbourne Melbourne Integrative Genomics, School of Mathematics and Statistics, , Melbourne, VIC 3052,"],"raw_orcid":"https://orcid.org/0000-0002-3818-1981","affiliations":[{"raw_affiliation_string":"University of Melbourne Melbourne Integrative Genomics, School of Mathematics and Statistics, , Melbourne, VIC 3052,","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210166212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5123830505","display_name":"Kris Sankaran","orcid":null},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kris Sankaran","raw_affiliation_strings":["University of Wisconsin-Madison Department of Statistics, , Madison, WI 53703,"],"raw_orcid":"https://orcid.org/0000-0002-9415-1971","affiliations":[{"raw_affiliation_string":"University of Wisconsin-Madison Department of Statistics, , Madison, WI 53703,","institution_ids":["https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065359043","https://openalex.org/A5086699730","https://openalex.org/A5123830505"],"corresponding_institution_ids":["https://openalex.org/I135310074","https://openalex.org/I165779595","https://openalex.org/I4210166212"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.32351246,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12157","display_name":"Geochemistry and Geologic Mapping","score":0.5418999791145325,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12157","display_name":"Geochemistry and Geologic Mapping","score":0.5418999791145325,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.04600000008940697,"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/T12417","display_name":"Morphological variations and asymmetry","score":0.03700000047683716,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.7888000011444092},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6014999747276306},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5831000208854675},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5702000260353088},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5386999845504761},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.5378000140190125},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics","score":0.49410000443458557}],"concepts":[{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.7888000011444092},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.713699996471405},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6014999747276306},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5831000208854675},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5702000260353088},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5386999845504761},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.5378000140190125},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.49410000443458557},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.4742000102996826},{"id":"https://openalex.org/C40866790","wikidata":"https://www.wikidata.org/wiki/Q956238","display_name":"Interactive computing","level":2,"score":0.4316999912261963},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.42649999260902405},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41749998927116394},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.36000001430511475},{"id":"https://openalex.org/C118965365","wikidata":"https://www.wikidata.org/wiki/Q44528","display_name":"Euclidean vector","level":2,"score":0.3513000011444092},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.3434000015258789},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33889999985694885},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3131999969482422},{"id":"https://openalex.org/C2984499602","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Computer software","level":2,"score":0.26190000772476196},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2565000057220459}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btag151","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag151","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:41883130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41883130","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag151","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag151","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1930591173","https://openalex.org/W2056279562","https://openalex.org/W2085926377","https://openalex.org/W2135415614","https://openalex.org/W2765573305","https://openalex.org/W2953915517","https://openalex.org/W3025053000","https://openalex.org/W3088375181","https://openalex.org/W3095016916","https://openalex.org/W3165782418","https://openalex.org/W3201917654","https://openalex.org/W3208089728","https://openalex.org/W4230085039","https://openalex.org/W4285207694","https://openalex.org/W4376132442","https://openalex.org/W4389146527","https://openalex.org/W4392973105","https://openalex.org/W4399077973","https://openalex.org/W4401442847","https://openalex.org/W4408099174","https://openalex.org/W4412380948","https://openalex.org/W7117582280"],"related_works":[],"abstract_inverted_index":{"SUMMARY:":[0],"Stacked":[1],"barplots,":[2],"though":[3],"widely":[4],"used":[5],"in":[6,13,78,97,105],"microbiome":[7,14],"studies,":[8],"can":[9,21,135,146],"obscure":[10],"important":[11],"patterns":[12],"data.":[15],"They":[16],"omit":[17],"rare":[18],"taxa":[19],"and":[20,64,144,158],"mask":[22],"shifts":[23],"that":[24,40,75],"emerge":[25],"at":[26,160],"finer":[27],"taxonomic":[28,49,73],"levels.":[29],"To":[30],"address":[31],"this":[32],"issue,":[33],"we":[34,95],"introduce":[35],"phylobar,":[36],"an":[37,115],"R":[38,116,139],"package":[39,117,154],"interactively":[41],"links":[42],"stacked":[43],"barplots":[44],"with":[45,83,87,130],"overview":[46],"phylogenetic":[47],"or":[48,57,141],"hierarchies.":[50],"The":[51,132,153],"interface":[52],"allows":[53,70],"users":[54],"to":[55,125],"collapse":[56],"expand":[58],"subtrees,":[59],"paint":[60],"color":[61],"palettes":[62],"interactively,":[63],"search":[65],"for":[66],"specific":[67],"taxa.":[68],"This":[69],"comparison":[71],"across":[72],"resolutions":[74],"are":[76],"hidden":[77],"static":[79],"overviews.":[80],"phylobar":[81,111],"works":[82],"any":[84],"omics":[85],"data":[86],"hierarchical":[88],"organization,":[89],"including":[90],"cell":[91,103],"type":[92],"hierarchies,":[93],"as":[94,114,149],"demonstrate":[96],"a":[98],"case":[99],"study":[100],"of":[101],"immune":[102],"composition":[104],"COVID-19":[106],"patients.":[107],"AVAILABILITY":[108],"AND":[109],"IMPLEMENTATION:":[110],"is":[112,155],"available":[113],"on":[118],"GitHub.":[119],"It":[120],"uses":[121],"the":[122],"htmlwidgets":[123],"library":[124],"link":[126],"interactive":[127,133],"D3":[128],"visualizations":[129],"R.":[131],"plots":[134],"be":[136,147],"embedded":[137],"within":[138],"Markdown":[140],"Quarto":[142],"notebooks,":[143],"views":[145],"exported":[148],"vector":[150],"graphics":[151],"files.":[152],"open":[156],"source":[157],"documented":[159],"https://mkdiro-O.github.io/phylobar.":[161]},"counts_by_year":[],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2026-03-27T00:00:00"}
