{"id":"https://openalex.org/W4200537204","doi":"https://doi.org/10.3390/app112311473","title":"\u2018SRS\u2019 R Package and \u2018q2-srs\u2019 QIIME 2 Plugin: Normalization of Microbiome Data Using Scaling with Ranked Subsampling (SRS)","display_name":"\u2018SRS\u2019 R Package and \u2018q2-srs\u2019 QIIME 2 Plugin: Normalization of Microbiome Data Using Scaling with Ranked Subsampling (SRS)","publication_year":2021,"publication_date":"2021-12-03","ids":{"openalex":"https://openalex.org/W4200537204","doi":"https://doi.org/10.3390/app112311473"},"language":"en","primary_location":{"id":"doi:10.3390/app112311473","doi":"https://doi.org/10.3390/app112311473","is_oa":true,"landing_page_url":"https://doi.org/10.3390/app112311473","pdf_url":"https://www.mdpi.com/2076-3417/11/23/11473/pdf?version=1638525137","source":{"id":"https://openalex.org/S4210205812","display_name":"Applied Sciences","issn_l":"2076-3417","issn":["2076-3417"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","norway-1","oarl","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Sciences","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2076-3417/11/23/11473/pdf?version=1638525137","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071783225","display_name":"Vitor Heidrich","orcid":"https://orcid.org/0000-0001-6617-9187","observed_orcids":["https://orcid.org/0000-0001-6617-9187"]},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"id":"https://openalex.org/I4210149843","display_name":"Hospital S\u00edrio-Liban\u00eas","ror":"https://ror.org/03r5mk904","country_code":"BR","type":"healthcare","lineage":["https://openalex.org/I4210149843"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Vitor Heidrich","raw_affiliation_strings":["Centro de Oncologia Molecular, Hospital S\u00edrio-Liban\u00eas, S\u00e3o Paulo 01308-060, Brazil","Departamento de Bioqu\u00edmica, Instituto de Qu\u00edmica, Universidade de S\u00e3o Paulo, S\u00e3o Paulo 05508-900, Brazil"],"raw_orcid":"https://orcid.org/0000-0001-6617-9187","affiliations":[{"raw_affiliation_string":"Centro de Oncologia Molecular, Hospital S\u00edrio-Liban\u00eas, S\u00e3o Paulo 01308-060, Brazil","institution_ids":["https://openalex.org/I4210149843"]},{"raw_affiliation_string":"Departamento de Bioqu\u00edmica, Instituto de Qu\u00edmica, Universidade de S\u00e3o Paulo, S\u00e3o Paulo 05508-900, Brazil","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056369912","display_name":"Petr Karlovsk\u00fd","orcid":"https://orcid.org/0000-0002-6532-5856","observed_orcids":["https://orcid.org/0000-0002-6532-5856"]},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Petr Karlovsky","raw_affiliation_strings":["Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, 37077 Goettingen, Germany"],"raw_orcid":"https://orcid.org/0000-0002-6532-5856","affiliations":[{"raw_affiliation_string":"Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, 37077 Goettingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036643919","display_name":"Lukas Beule","orcid":"https://orcid.org/0000-0003-1107-7540","observed_orcids":["https://orcid.org/0000-0003-1107-7540"]},"institutions":[{"id":"https://openalex.org/I1326965316","display_name":"Julius K\u00fchn-Institut","ror":"https://ror.org/022d5qt08","country_code":"DE","type":"government","lineage":["https://openalex.org/I1326965316","https://openalex.org/I2801963157"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Lukas Beule","raw_affiliation_strings":["Julius K\u00fchn Institute (JKI)\u2014Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, 14195 Berlin, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1107-7540","affiliations":[{"raw_affiliation_string":"Julius K\u00fchn Institute (JKI)\u2014Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, 14195 Berlin, Germany","institution_ids":["https://openalex.org/I1326965316"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5036643919","https://openalex.org/A5071783225"],"corresponding_institution_ids":["https://openalex.org/I1326965316","https://openalex.org/I17974374","https://openalex.org/I4210149843"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2160},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2160},"fwci":5.3429,"has_fulltext":true,"cited_by_count":74,"citation_normalized_percentile":{"value":0.97004637,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"11","issue":"23","first_page":"11473","last_page":"11473"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.5781000256538391,"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"}},"topics":[{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.5781000256538391,"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":0.14390000700950623,"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/T10066","display_name":"Gut microbiota and health","score":0.10970000177621841,"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/sampling-bias","display_name":"sampling bias","score":0.5090000033378601},{"id":"https://openalex.org/keywords/count-data","display_name":"count data","score":0.6470000147819519},{"id":"https://openalex.org/keywords/reproducibility","display_name":"reproducibility","score":0.5770000219345093}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.7141368985176086},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.6574856042861938},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5923702716827393},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.531719446182251},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.4845823049545288},{"id":"https://openalex.org/C33643355","wikidata":"https://www.wikidata.org/wiki/Q5176731","display_name":"Count data","level":3,"score":0.44634270668029785},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4256017208099365},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.416154682636261},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3855818212032318},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.28892576694488525},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.2480635643005371},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20076340436935425},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15489771962165833},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.13149461150169373},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.12082463502883911},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3390/app112311473","doi":"https://doi.org/10.3390/app112311473","is_oa":true,"landing_page_url":"https://doi.org/10.3390/app112311473","pdf_url":"https://www.mdpi.com/2076-3417/11/23/11473/pdf?version=1638525137","source":{"id":"https://openalex.org/S4210205812","display_name":"Applied Sciences","issn_l":"2076-3417","issn":["2076-3417"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","norway-1","oarl","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Sciences","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:dea5e3ec67bf468f9d852c94c88a6d30","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/dea5e3ec67bf468f9d852c94c88a6d30","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,"listed_in":[],"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":"Applied Sciences, Vol 11, Iss 23, p 11473 (2021)","raw_type":"article"},{"id":"pmh:oai:publications.goettingen-research-online.de:2/98926","doi":null,"is_oa":true,"landing_page_url":"https://resolver.sub.uni-goettingen.de/purl?gro-2/98926","pdf_url":null,"source":{"id":"https://openalex.org/S4306401634","display_name":"GoeScholar  The Publication Server of the Georg-August-Universit\u00e4t G\u00f6ttingen (Georg-August-Universit\u00e4t G\u00f6ttingen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210122495","host_organization_name":"Asklepios Klinik St. Georg","host_organization_lineage":["https://openalex.org/I4210122495"],"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":"","raw_type":"journal_article"},{"id":"pmh:oai:www.openagrar.de:openagrar_mods_00076321","doi":null,"is_oa":true,"landing_page_url":"https://www.openagrar.de/receive/openagrar_mods_00076321","pdf_url":null,"source":{"id":"https://openalex.org/S7407055137","display_name":"OpenAgrar","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/app112311473","doi":"https://doi.org/10.3390/app112311473","is_oa":true,"landing_page_url":"https://doi.org/10.3390/app112311473","pdf_url":"https://www.mdpi.com/2076-3417/11/23/11473/pdf?version=1638525137","source":{"id":"https://openalex.org/S4210205812","display_name":"Applied Sciences","issn_l":"2076-3417","issn":["2076-3417"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","norway-1","oarl","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Sciences","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1212980931","display_name":"BonaRes (Modul A, Phase 2): SIGNAL - Nachhaltige Intensivierung der Landwirtschaft durch Agroforstsysteme, Teilprojekt A","funder_award_id":"031B0510A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G328380941","display_name":null,"funder_award_id":"13996-0/2018","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G6648539501","display_name":"BonaRes (Modul A): SIGNAL - Nachhaltige Intensivierung der Landwirtschaft durch Agroforstsysteme, Teilprojekt A","funder_award_id":"031A562A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4200537204.pdf","grobid_xml":"https://content.openalex.org/works/W4200537204.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2004014148","https://openalex.org/W2162088497","https://openalex.org/W2748607273","https://openalex.org/W2805044645","https://openalex.org/W2810951606","https://openalex.org/W2963276645","https://openalex.org/W3046751398","https://openalex.org/W3137718280","https://openalex.org/W3174993126","https://openalex.org/W3176237781","https://openalex.org/W3213132551","https://openalex.org/W4226158954"],"related_works":["https://openalex.org/W3046751398","https://openalex.org/W3144154879","https://openalex.org/W2970474980","https://openalex.org/W4386356775","https://openalex.org/W7212472141","https://openalex.org/W2898942477","https://openalex.org/W6948158701","https://openalex.org/W4410600065","https://openalex.org/W4402582261","https://openalex.org/W7133091780"],"abstract_inverted_index":{"Several":[0],"ecological":[1,32],"data":[2,34],"types,":[3],"especially":[4],"microbiome":[5],"count":[6,33],"data,":[7],"are":[8],"commonly":[9],"sample-wise":[10],"normalized":[11],"before":[12],"analysis":[13],"to":[14,88],"correct":[15],"for":[16,28,85,94],"sampling":[17],"bias":[18],"and":[19,53,74],"other":[20],"technical":[21],"artifacts.":[22],"Recently,":[23],"we":[24,61],"developed":[25],"an":[26,63],"algorithm":[27,68],"the":[29,43,56,66,70,75,90],"normalization":[30],"of":[31,65,92],"called":[35],"\u2018scaling":[36],"with":[37],"ranked":[38],"subsampling":[39,48],"(SRS)\u2019,":[40],"which":[41],"surpasses":[42],"widely":[44],"adopted":[45],"\u2018rarefying\u2019":[46],"(random":[47],"without":[49],"replacement)":[50],"in":[51,54,69],"reproducibility":[52],"safeguarding":[55],"original":[57],"community":[58],"structure.":[59],"Here,":[60],"describe":[62],"implementation":[64],"SRS":[67],"\u2018SRS\u2019":[71],"R":[72],"package":[73],"\u2018q2-srs\u2019":[76],"QIIME":[77],"2":[78],"plugin.":[79],"We":[80],"also":[81],"provide":[82],"accessory":[83],"functions":[84],"dataset":[86],"exploration":[87],"guide":[89],"choice":[91],"parameters":[93],"SRS.":[95]},"counts_by_year":[{"year":2026,"cited_by_count":15},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":11}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2021-12-31T00:00:00"}
