FlowDiv: A new pipeline for analyzing flow cytometric diversity

Autores
Wanderley, Bruno M. S.; Araújo, Daniel S.; Quiroga, María Victoria; Amado, André M.; Neto, Adrião D. D.; Sarmento, Hugo; Metz, Sebastián Darío; Unrein, Fernando
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Flow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide applicability led to the development of various analytical protocols, which are often not interchangeable between fields of expertise. Environmental science in particular faces difficulty in adapting to non-specific protocols, mainly because of the highly heterogeneous nature of environmental samples. This variety, although it is intrinsic to environmental studies, makes it difficult to adjust analytical protocols to maintain both mathematical formalism and comprehensible biological interpretations, principally for questions that rely on the evaluation of differences between cytograms, an approach also termed cytometric diversity. Despite the availability of promising bioinformatic tools conceived for or adapted to cytometric diversity, most of them still cannot deal with common technical issues such as the integration of differently acquired datasets, the optimal number of bins, and the effective correlation of bins to previously known cytometric populations. Results: To address these and other questions, we have developed flowDiv, an R language pipeline for analysis of environmental flow cytometry data. Here, we present the rationale for flowDiv and apply the method to a real dataset from 31 freshwater lakes in Patagonia, Argentina, to reveal significant aspects of their cytometric diversities. Conclusions: flowDiv provides a rather intuitive way of proceeding with FCM analysis, as it combines formal mathematical solutions and biological rationales in an intuitive framework specifically designed to explore cytometric diversity.
Fil: Wanderley, Bruno M. S.. Universidade Federal do Rio Grande do Norte; Brasil
Fil: Araújo, Daniel S.. Universidade Federal do Rio Grande do Norte; Brasil
Fil: Quiroga, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Amado, André M.. Universidade Federal do Rio Grande do Norte; Brasil. Universidade Federal de Juiz de Fora; Brasil
Fil: Neto, Adrião D. D.. Universidade Federal do Rio Grande do Norte; Brasil
Fil: Sarmento, Hugo. Universidade Federal do São Carlos; Brasil
Fil: Metz, Sebastián Darío. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Unrein, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Materia
CYTOMETRIC DIVERSITY
FLOW CYTOMETRY
R LANGUAGE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/118998
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/118998
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling FlowDiv: A new pipeline for analyzing flow cytometric diversityWanderley, Bruno M. S.Araújo, Daniel S.Quiroga, María VictoriaAmado, André M.Neto, Adrião D. D.Sarmento, HugoMetz, Sebastián DaríoUnrein, FernandoCYTOMETRIC DIVERSITYFLOW CYTOMETRYR LANGUAGEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: Flow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide applicability led to the development of various analytical protocols, which are often not interchangeable between fields of expertise. Environmental science in particular faces difficulty in adapting to non-specific protocols, mainly because of the highly heterogeneous nature of environmental samples. This variety, although it is intrinsic to environmental studies, makes it difficult to adjust analytical protocols to maintain both mathematical formalism and comprehensible biological interpretations, principally for questions that rely on the evaluation of differences between cytograms, an approach also termed cytometric diversity. Despite the availability of promising bioinformatic tools conceived for or adapted to cytometric diversity, most of them still cannot deal with common technical issues such as the integration of differently acquired datasets, the optimal number of bins, and the effective correlation of bins to previously known cytometric populations. Results: To address these and other questions, we have developed flowDiv, an R language pipeline for analysis of environmental flow cytometry data. Here, we present the rationale for flowDiv and apply the method to a real dataset from 31 freshwater lakes in Patagonia, Argentina, to reveal significant aspects of their cytometric diversities. Conclusions: flowDiv provides a rather intuitive way of proceeding with FCM analysis, as it combines formal mathematical solutions and biological rationales in an intuitive framework specifically designed to explore cytometric diversity.Fil: Wanderley, Bruno M. S.. Universidade Federal do Rio Grande do Norte; BrasilFil: Araújo, Daniel S.. Universidade Federal do Rio Grande do Norte; BrasilFil: Quiroga, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Amado, André M.. Universidade Federal do Rio Grande do Norte; Brasil. Universidade Federal de Juiz de Fora; BrasilFil: Neto, Adrião D. D.. Universidade Federal do Rio Grande do Norte; BrasilFil: Sarmento, Hugo. Universidade Federal do São Carlos; BrasilFil: Metz, Sebastián Darío. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Unrein, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaBioMed Central2019-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/118998Wanderley, Bruno M. S.; Araújo, Daniel S.; Quiroga, María Victoria; Amado, André M.; Neto, Adrião D. D.; et al.; FlowDiv: A new pipeline for analyzing flow cytometric diversity; BioMed Central; BMC Bioinformatics; 20; 1; 5-2019; 1-101471-2105CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-019-2787-4info:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2787-4info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:32:56Zoai:ri.conicet.gov.ar:11336/118998instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:32:56.548CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv FlowDiv: A new pipeline for analyzing flow cytometric diversity
title FlowDiv: A new pipeline for analyzing flow cytometric diversity
spellingShingle FlowDiv: A new pipeline for analyzing flow cytometric diversity
Wanderley, Bruno M. S.
CYTOMETRIC DIVERSITY
FLOW CYTOMETRY
R LANGUAGE
title_short FlowDiv: A new pipeline for analyzing flow cytometric diversity
title_full FlowDiv: A new pipeline for analyzing flow cytometric diversity
title_fullStr FlowDiv: A new pipeline for analyzing flow cytometric diversity
title_full_unstemmed FlowDiv: A new pipeline for analyzing flow cytometric diversity
title_sort FlowDiv: A new pipeline for analyzing flow cytometric diversity
dc.creator.none.fl_str_mv Wanderley, Bruno M. S.
Araújo, Daniel S.
Quiroga, María Victoria
Amado, André M.
Neto, Adrião D. D.
Sarmento, Hugo
Metz, Sebastián Darío
Unrein, Fernando
author Wanderley, Bruno M. S.
author_facet Wanderley, Bruno M. S.
Araújo, Daniel S.
Quiroga, María Victoria
Amado, André M.
Neto, Adrião D. D.
Sarmento, Hugo
Metz, Sebastián Darío
Unrein, Fernando
author_role author
author2 Araújo, Daniel S.
Quiroga, María Victoria
Amado, André M.
Neto, Adrião D. D.
Sarmento, Hugo
Metz, Sebastián Darío
Unrein, Fernando
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv CYTOMETRIC DIVERSITY
FLOW CYTOMETRY
R LANGUAGE
topic CYTOMETRIC DIVERSITY
FLOW CYTOMETRY
R LANGUAGE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: Flow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide applicability led to the development of various analytical protocols, which are often not interchangeable between fields of expertise. Environmental science in particular faces difficulty in adapting to non-specific protocols, mainly because of the highly heterogeneous nature of environmental samples. This variety, although it is intrinsic to environmental studies, makes it difficult to adjust analytical protocols to maintain both mathematical formalism and comprehensible biological interpretations, principally for questions that rely on the evaluation of differences between cytograms, an approach also termed cytometric diversity. Despite the availability of promising bioinformatic tools conceived for or adapted to cytometric diversity, most of them still cannot deal with common technical issues such as the integration of differently acquired datasets, the optimal number of bins, and the effective correlation of bins to previously known cytometric populations. Results: To address these and other questions, we have developed flowDiv, an R language pipeline for analysis of environmental flow cytometry data. Here, we present the rationale for flowDiv and apply the method to a real dataset from 31 freshwater lakes in Patagonia, Argentina, to reveal significant aspects of their cytometric diversities. Conclusions: flowDiv provides a rather intuitive way of proceeding with FCM analysis, as it combines formal mathematical solutions and biological rationales in an intuitive framework specifically designed to explore cytometric diversity.
Fil: Wanderley, Bruno M. S.. Universidade Federal do Rio Grande do Norte; Brasil
Fil: Araújo, Daniel S.. Universidade Federal do Rio Grande do Norte; Brasil
Fil: Quiroga, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Amado, André M.. Universidade Federal do Rio Grande do Norte; Brasil. Universidade Federal de Juiz de Fora; Brasil
Fil: Neto, Adrião D. D.. Universidade Federal do Rio Grande do Norte; Brasil
Fil: Sarmento, Hugo. Universidade Federal do São Carlos; Brasil
Fil: Metz, Sebastián Darío. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Unrein, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
description Background: Flow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide applicability led to the development of various analytical protocols, which are often not interchangeable between fields of expertise. Environmental science in particular faces difficulty in adapting to non-specific protocols, mainly because of the highly heterogeneous nature of environmental samples. This variety, although it is intrinsic to environmental studies, makes it difficult to adjust analytical protocols to maintain both mathematical formalism and comprehensible biological interpretations, principally for questions that rely on the evaluation of differences between cytograms, an approach also termed cytometric diversity. Despite the availability of promising bioinformatic tools conceived for or adapted to cytometric diversity, most of them still cannot deal with common technical issues such as the integration of differently acquired datasets, the optimal number of bins, and the effective correlation of bins to previously known cytometric populations. Results: To address these and other questions, we have developed flowDiv, an R language pipeline for analysis of environmental flow cytometry data. Here, we present the rationale for flowDiv and apply the method to a real dataset from 31 freshwater lakes in Patagonia, Argentina, to reveal significant aspects of their cytometric diversities. Conclusions: flowDiv provides a rather intuitive way of proceeding with FCM analysis, as it combines formal mathematical solutions and biological rationales in an intuitive framework specifically designed to explore cytometric diversity.
publishDate 2019
dc.date.none.fl_str_mv 2019-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/118998
Wanderley, Bruno M. S.; Araújo, Daniel S.; Quiroga, María Victoria; Amado, André M.; Neto, Adrião D. D.; et al.; FlowDiv: A new pipeline for analyzing flow cytometric diversity; BioMed Central; BMC Bioinformatics; 20; 1; 5-2019; 1-10
1471-2105
CONICET Digital
CONICET
url http://hdl.handle.net/11336/118998
identifier_str_mv Wanderley, Bruno M. S.; Araújo, Daniel S.; Quiroga, María Victoria; Amado, André M.; Neto, Adrião D. D.; et al.; FlowDiv: A new pipeline for analyzing flow cytometric diversity; BioMed Central; BMC Bioinformatics; 20; 1; 5-2019; 1-10
1471-2105
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-019-2787-4
info:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2787-4
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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