Journal of Open Source Software Paper

JOSS/paper.bib

+@article{animalcules,
+  title        = {animalcules: interactive microbiome analytics and visualization in R},
+  author       = {Yue Zhao and Anthony Federico and Tyler Faits and Solaiappan Manimaran and Daniel Segrè and Stefano Monti and W. Evan Johnson},
+  year         = 2021,
+  month        = mar,
+  journal      = {Microbiome},
+  publisher    = {Springer Science and Business Media {LLC}},
+  volume       = 9,
+  number       = 1,
+  doi          = {10.1186/s40168-021-01013-0},
+  url          = {https://doi.org/10.1186/s40168-021-01013-0}
+}
+
+@article{Chaillou2014,
+  title        = {Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage},
+  author       = {Stéphane Chaillou and Aurélie Chaulot-Talmon and Hélène Caekebeke and Mireille Cardinal and Souad Christieans and Catherine Denis and Marie Hélène Desmonts and Xavier Dousset and Carole Feurer and Erwann Hamon and Jean-Jacques Joffraud and Stéphanie La Carbona and Françoise Leroi and Sabine Leroy and Sylvie Lorre and Sabrina Macé and Marie-France Pilet and Hervé Prévost and Marina Rivollier and Dephine Roux and Régine Talon and Monique Zagorec and Marie-Christine Champomier-Vergès},
+  year         = 2014,
+  month        = oct,
+  journal      = {The {ISME} Journal},
+  publisher    = {Springer Science and Business Media {LLC}},
+  volume       = 9,
+  number       = 5,
+  pages        = {1105--1118},
+  doi          = {10.1038/ismej.2014.202},
+  url          = {https://doi.org/10.1038/ismej.2014.202}
+}
+
+@article{DADA2,
+  title        = {{DADA}2: High-resolution sample inference from Illumina amplicon data},
+  author       = {Benjamin J Callahan and Paul J McMurdie and Michael J Rosen and Andrew W Han and Amy Jo A Johnson and Susan P Holmes},
+  year         = 2016,
+  month        = may,
+  journal      = {Nature Methods},
+  publisher    = {Springer Science and Business Media {LLC}},
+  volume       = 13,
+  number       = 7,
+  pages        = {581--583},
+  doi          = {10.1038/nmeth.3869},
+  url          = {https://doi.org/10.1038/nmeth.3869}
+}
+
+@article{FROGS,
+  title        = {{FROGS}: Find,  Rapidly,  {OTUs} with Galaxy Solution},
+  author       = {Frédéric Escudié and Lucas Auer and Maria Bernard and Mahendra Mariadassou and Laurent Cauquil and Katia Vidal and Sarah Maman and Guillermina Hernandez-Raquet and Sylvie Combes and Géraldine Pascal},
+  year         = 2017,
+  month        = dec,
+  journal      = {Bioinformatics},
+  publisher    = {Oxford University Press ({OUP})},
+  volume       = 34,
+  number       = 8,
+  pages        = {1287--1294},
+  doi          = {10.1093/bioinformatics/btx791},
+  url          = {https://doi.org/10.1093/bioinformatics/btx791},
+  editor       = {Bonnie Berger}
+}
+
+@article{FROGS-ITS,
+  title        = {{FROGS}: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers},
+  author       = {Maria Bernard and Olivier Rué and Mahendra Mariadassou and Géraldine Pascal},
+  year         = 2021,
+  month        = aug,
+  journal      = {Briefings in Bioinformatics},
+  publisher    = {Oxford University Press ({OUP})},
+  doi          = {10.1093/bib/bbab318},
+  url          = {https://doi.org/10.1093/bib/bbab318}
+}
+
+@article{Karimi2020,
+  title        = {Biogeography of soil microbial habitats across France},
+  author       = {Battle Karimi and Jean Villerd and Samuel Dequiedt and Sébastien Terrat and Nicolas Chemidlin-Prévost Bouré and Christophe Djemiel and Mélanie Lelièvre and Julie Tripied and Virginie Nowak and Nicolas P. A. Saby and Antonio Bispo and Claudy Jolivet and Dominique Arrouays and Patrick Wincker and Corinne Cruaud and Lionel Ranjard},
+  year         = 2020,
+  month        = may,
+  journal      = {Global Ecology and Biogeography},
+  publisher    = {Wiley},
+  volume       = 29,
+  number       = 8,
+  pages        = {1399--1411},
+  doi          = {10.1111/geb.13118},
+  url          = {https://doi.org/10.1111/geb.13118},
+  editor       = {Edward Mitchell}
+}
+
+@article{LeChatelier2013,
+  title        = {Richness of human gut microbiome correlates with metabolic markers},
+  author       = {Emmanuelle Le Chatelier and   and Trine Nielsen and Junjie Qin and Edi Prifti and Falk Hildebrand and Gwen Falony and Mathieu Almeida and Manimozhiyan Arumugam and Jean-Michel Batto and Sean Kennedy and Pierre Leonard and Junhua Li and Kristoffer Burgdorf and Niels Grarup and Torben Jørgensen and Ivan Brandslund and Henrik Bjørn Nielsen and Agnieszka S. Juncker and Marcelo Bertalan and Florence Levenez and Nicolas Pons and Simon Rasmussen and Shinichi Sunagawa and Julien Tap and Sebastian Tims and Erwin G. Zoetendal and Søren Brunak and Karine Clément and Joël Doré and Michiel Kleerebezem and Karsten Kristiansen and Pierre Renault and Thomas Sicheritz-Ponten and Willem M. de Vos and Jean-Daniel Zucker and Jeroen Raes and Torben Hansen and Peer Bork and Jun Wang and S. Dusko Ehrlich and Oluf Pedersen},
+  year         = 2013,
+  month        = aug,
+  journal      = {Nature},
+  publisher    = {Springer Science and Business Media {LLC}},
+  volume       = 500,
+  number       = 7464,
+  pages        = {541--546},
+  doi          = {10.1038/nature12506},
+  url          = {https://doi.org/10.1038/nature12506}
+}
+
+@article{metacoder,
+  title        = {Metacoder: An R package for visualization and manipulation of community taxonomic diversity data},
+  author       = {Zachary S. L. Foster and Thomas J. Sharpton and Niklaus J. Grünwald},
+  year         = 2017,
+  month        = feb,
+  journal      = {{PLOS} Computational Biology},
+  publisher    = {Public Library of Science ({PLoS})},
+  volume       = 13,
+  number       = 2,
+  pages        = {e1005404},
+  doi          = {10.1371/journal.pcbi.1005404},
+  url          = {https://doi.org/10.1371/journal.pcbi.1005404},
+  editor       = {Timothée Poisot}
+}
+
+@misc{microbiome,
+  title        = {microbiome R package},
+  author       = {Leo Lahti and Sudarshan Shetty},
+  year         = {2012-2019}
+}
+
+@misc{MIGALE,
+  title        = {Migale Bioinformatics Facility},
+  author       = {{MIGALE}},
+  year         = 2018,
+  publisher    = {INRAE},
+  doi          = {10.15454/1.5572390655343293E12},
+}
+
+@article{phyloseq,
+  title        = {phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data},
+  author       = {Paul J. McMurdie and Susan Holmes},
+  year         = 2013,
+  month        = apr,
+  journal      = {{PLoS ONE}},
+  publisher    = {Public Library of Science ({PLoS})},
+  volume       = 8,
+  number       = 4,
+  pages        = {e61217},
+  doi          = {10.1371/journal.pone.0061217},
+  url          = {https://doi.org/10.1371/journal.pone.0061217},
+  editor       = {Michael Watson}
+}
+
+@article{Poirier2016,
+  title        = {Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators?},
+  author       = {Simon Poirier and Ariane Bize and Chrystelle Bureau and Théodore Bouchez and Olivier Chapleur},
+  year         = 2016,
+  month        = sep,
+  journal      = {Water Research},
+  publisher    = {Elsevier {BV}},
+  volume       = 100,
+  pages        = {296--305},
+  doi          = {10.1016/j.watres.2016.05.041},
+  url          = {https://doi.org/10.1016/j.watres.2016.05.041}
+}
+
+@article{QIIME,
+  title        = {{QIIME} allows analysis of high-throughput community sequencing data},
+  author       = {J Gregory Caporaso and Justin Kuczynski and Jesse Stombaugh and Kyle Bittinger and Frederic D Bushman and Elizabeth K Costello and Noah Fierer and Antonio Gonzalez Peña and Julia K Goodrich and Jeffrey I Gordon and Gavin A Huttley and Scott T Kelley and Dan Knights and Jeremy E Koenig and Ruth E Ley and Catherine A Lozupone and Daniel McDonald and Brian D Muegge and Meg Pirrung and Jens Reeder and Joel R Sevinsky and Peter J Turnbaugh and William A Walters and Jeremy Widmann and Tanya Yatsunenko and Jesse Zaneveld and Rob Knight},
+  year         = 2010,
+  month        = apr,
+  journal      = {Nature Methods},
+  publisher    = {Springer Science and Business Media {LLC}},
+  volume       = 7,
+  number       = 5,
+  pages        = {335--336},
+  doi          = {10.1038/nmeth.f.303},
+  url          = {https://doi.org/10.1038/nmeth.f.303}
+}
+
+@article{shaman,
+  title        = {{SHAMAN}: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis},
+  author       = {Stevenn Volant and Pierre Lechat and Perrine Woringer and Laurence Motreff and Pascal Campagne and Christophe Malabat and Sean Kennedy and Amine Ghozlane},
+  year         = 2020,
+  month        = aug,
+  journal      = {{BMC} Bioinformatics},
+  publisher    = {Springer Science and Business Media {LLC}},
+  volume       = 21,
+  number       = 1,
+  doi          = {10.1186/s12859-020-03666-4},
+  url          = {https://doi.org/10.1186/s12859-020-03666-4}
+}
+
+@manual{shiny,
+  title        = {shiny: Web Application Framework for R},
+  author       = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
+  year         = 2021,
+  url          = {https://CRAN.R-project.org/package=shiny},
+  note         = {R package version 1.6.0}
+}
+
+@article{shiny-phyloseq,
+  title        = {Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking},
+  author       = {P. J. McMurdie and S. Holmes},
+  year         = 2014,
+  month        = sep,
+  journal      = {Bioinformatics},
+  publisher    = {Oxford University Press ({OUP})},
+  volume       = 31,
+  number       = 2,
+  pages        = {282--283},
+  doi          = {10.1093/bioinformatics/btu616},
+  url          = {https://doi.org/10.1093/bioinformatics/btu616}
+}
+
+@manual{shinymeta,
+  title        = {shinymeta: Export Domain Logic from Shiny using Meta-Programming},
+  author       = {Joe Cheng and Carson Sievert},
+  year         = 2021,
+  url          = {https://CRAN.R-project.org/package=shinymeta},
+  note         = {R package version 0.2.0.1}
+}