{"id":"https://openalex.org/W3126727125","doi":"https://doi.org/10.1186/s12859-021-03967-2","title":"tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R","display_name":"tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R","publication_year":2021,"publication_date":"2021-02-01","ids":{"openalex":"https://openalex.org/W3126727125","doi":"https://doi.org/10.1186/s12859-021-03967-2","mag":"3126727125","pmid":"https://pubmed.ncbi.nlm.nih.gov/33526006"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-03967-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03967-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-03967-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-03967-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061426767","display_name":"Charlie M. Carpenter","orcid":"https://orcid.org/0000-0002-4698-1516"},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Charlie M. Carpenter","raw_affiliation_strings":["Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. charles.carpenter@cuanschutz.edu","Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA"],"raw_orcid":"https://orcid.org/0000-0002-4698-1516","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. charles.carpenter@cuanschutz.edu","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]},{"raw_affiliation_string":"Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065375575","display_name":"Daniel N. Frank","orcid":"https://orcid.org/0000-0001-6669-228X"},"institutions":[{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel N. Frank","raw_affiliation_strings":["Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Denver, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Denver, CO, USA","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030670818","display_name":"Kayla Williamson","orcid":"https://orcid.org/0000-0002-8302-5558"},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kayla Williamson","raw_affiliation_strings":["Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001400701","display_name":"Jaron Arbet","orcid":"https://orcid.org/0000-0003-4218-2458"},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jaron Arbet","raw_affiliation_strings":["Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072220989","display_name":"Brandie D. Wagner","orcid":"https://orcid.org/0000-0002-2745-0103"},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brandie D. Wagner","raw_affiliation_strings":["Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022404035","display_name":"Katerina Kechris","orcid":"https://orcid.org/0000-0002-3725-5459"},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katerina Kechris","raw_affiliation_strings":["Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015457989","display_name":"Miranda Kroehl","orcid":"https://orcid.org/0000-0002-3840-3660"},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Miranda E. Kroehl","raw_affiliation_strings":["Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5061426767"],"corresponding_institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.2583,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.78590312,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"41","last_page":"41"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.6168000102043152,"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/T10066","display_name":"Gut microbiota and health","score":0.6168000102043152,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.1500999927520752,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.03750000149011612,"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/computer-science","display_name":"Computer science","score":0.6687682867050171},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6615817546844482},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.5901745557785034},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5638299584388733},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.548281192779541},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.5275048017501831},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5007567405700684},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.47228771448135376},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4592651128768921},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24266573786735535},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22465288639068604},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2026273012161255},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1795375645160675}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6687682867050171},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6615817546844482},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.5901745557785034},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5638299584388733},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.548281192779541},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.5275048017501831},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5007567405700684},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.47228771448135376},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4592651128768921},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24266573786735535},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22465288639068604},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2026273012161255},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1795375645160675},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","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":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-021-03967-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03967-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-03967-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33526006","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33526006","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:a4a19f4ca003442b937182b3d0767559","is_oa":true,"landing_page_url":"https://doaj.org/article/a4a19f4ca003442b937182b3d0767559","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-13 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:6763733","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC7852128","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7852128","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7852128","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-03967-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03967-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-03967-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.44999998807907104}],"awards":[{"id":"https://openalex.org/G1428580439","display_name":null,"funder_award_id":"DK101659","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6673148089","display_name":null,"funder_award_id":"DK114711","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7135903733","display_name":null,"funder_award_id":"TR001082","funder_id":"https://openalex.org/F4320333634","funder_display_name":"Anschutz Medical Campus, University of Colorado"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320333634","display_name":"Anschutz Medical Campus, University of Colorado","ror":"https://ror.org/03wmf1y16"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3126727125.pdf","grobid_xml":"https://content.openalex.org/works/W3126727125.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1818557889","https://openalex.org/W1963826206","https://openalex.org/W2030030445","https://openalex.org/W2074266761","https://openalex.org/W2096442585","https://openalex.org/W2108718991","https://openalex.org/W2166948169","https://openalex.org/W2179438025","https://openalex.org/W2582567538","https://openalex.org/W2904250115","https://openalex.org/W2955435388","https://openalex.org/W2963276645","https://openalex.org/W2979464486","https://openalex.org/W2990427812"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W4390569940","https://openalex.org/W2888392564","https://openalex.org/W4361193272","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W2806259446","https://openalex.org/W2963326959","https://openalex.org/W4312407344","https://openalex.org/W2894289927"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,18,258],"drive":[2],"to":[3,68,79,82,110,122,178,199,202,213,226,245,253,271],"understand":[4],"how":[5],"microbial":[6,25],"communities":[7,26],"interact":[8],"with":[9,50,160],"their":[10,64],"environments":[11],"has":[12],"inspired":[13],"innovations":[14],"across":[15],"many":[16],"fields.":[17],"data":[19,36,66,74,84,196,273],"generated":[20],"from":[21,93,264],"sequence-based":[22],"analyses":[23,104,111,244],"of":[24,29,39,112,137,148],"typically":[27],"are":[28,267],"high":[30,47],"dimensionality":[31],"and":[32,87,105,155,175,261,269],"can":[33,53],"involve":[34],"multiple":[35,46,161],"tables":[37,49],"consisting":[38],"taxonomic":[40],"or":[41,85],"functional":[42],"gene/pathway":[43],"counts.":[44],"Merging":[45],"dimensional":[48],"study-related":[51],"metadata":[52],"be":[54,77],"challenging.":[55],"Existing":[56,96],"microbiome":[57,83,128,192,228],"pipelines":[58],"available":[59,141],"in":[60,142,217,231],"R":[61,86,119,200],"have":[62],"created":[63],"own":[65],"structures":[67,75,197],"manage":[69],"this":[70],"problem.":[71],"However,":[72],"these":[73],"may":[76],"unfamiliar":[78],"analysts":[80],"new":[81,215],"do":[88],"not":[89],"allow":[90],"for":[91,163,191],"deviations":[92],"internal":[94],"workflows.":[95],"analysis":[97,129,193,218,229],"tools":[98,140,236],"also":[99,194],"focus":[100],"primarily":[101],"on":[102,242],"community-level":[103],"exploratory":[106,153],"visualizations,":[107,154],"as":[108,124,237,239],"opposed":[109],"individual":[113],"taxa.":[114],"RESULTS:":[115],"We":[116,233],"developed":[117],"the":[118,138,265],"package":[120,266],"\"tidyMicro\"":[121],"serve":[123],"a":[125,223],"more":[126],"complete":[127,209],"pipeline.":[130],"This":[131,188],"open":[132,255],"source":[133,256],"software":[134],"provides":[135,222],"all":[136],"essential":[139],"other":[143],"popular":[144,227],"packages":[145,230],"(e.g.,":[146,166,181],"management":[147],"sequence":[149],"count":[150],"tables,":[151],"standard":[152,235,243],"diversity":[156],"inference":[157],"tools)":[158],"supplemented":[159],"options":[162],"regression":[164],"modelling":[165],"negative":[167],"binomial,":[168,170],"beta":[169],"and/or":[171],"rank":[172],"based":[173],"testing)":[174],"novel":[176,240],"visualizations":[177],"improve":[179,203,246],"interpretability":[180,247],"Rocky":[182],"Mountain":[183],"plots,":[184],"longitudinal":[185],"ordination":[186],"plots).":[187],"comprehensive":[189],"pipeline":[190],"maintains":[195],"familiar":[198],"users":[201,216],"analysts'":[204],"control":[205],"over":[206],"workflow.":[207,219],"A":[208],"vignette":[210],"is":[211],"provided":[212],"aid":[214],"CONCLUSIONS:":[220],"tidyMicro":[221],"reliable":[224],"alternative":[225],"R.":[232],"provide":[234],"well":[238],"extensions":[241],"results":[248],"while":[249],"maintaining":[250],"object":[251],"malleability":[252],"encourage":[254],"collaboration.":[257],"simple":[259],"examples":[260],"full":[262],"workflow":[263],"reproducible":[268],"applicable":[270],"external":[272],"sets.":[274]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
