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@Article{Betaregression_2010,
title = {Beta Regression in {R}},
author = {Francisco Cribari-Neto and Achim Zeileis},
journal = {Journal of Statistical Software},
year = {2010},
volume = {34},
number = {2},
pages = {1-24},
doi = {10.18637/jss.v034.i02},
}
@article{Liu_meconetcomp_2023,
author = {Liu, Chi and Li, Chaonan and Jiang, Yanqiong and Zeng, Raymond J. and Yao, Minjie and Li, Xiangzhen},
title = {A guide for comparing microbial co-occurrence networks},
journal = {iMeta},
pages = {e71},
DOI = {10.1002/imt2.71},
year = {2023},
type = {Journal Article}
}
@article{Buttigieg_guide_2014,
author = {Buttigieg, Pier Luigi and Ramette, Alban},
title = {A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses},
journal = {FEMS Microbiology Ecology},
volume = {90},
number = {3},
pages = {543-550},
ISSN = {0168-6496},
DOI = {10.1111/1574-6941.12437},
url = {https://doi.org/10.1111/1574-6941.12437},
year = {2014},
type = {Journal Article}
}
@article{Dietrich_Namco_2022,
author = {Dietrich, A. and Matchado, M. S. and Zwiebel, M. and Olke, B. and Lauber, M. and Lagkouvardos, I. and Baumbach, J. and Haller, D. and Brandl, B. and Skurk, T. and Hauner, H. and Reitmeier, S. and List, M.},
title = {Namco: a microbiome explorer},
journal = {Microbial genomics},
volume = {8},
number = {8},
pages = {000852},
DOI = {10.1099/mgen.0.000852},
url = {http://www.ncbi.nlm.nih.gov/pubmed/35917163},
year = {2022},
type = {Journal Article}
}
@article{Fernandes_Unifying_2014,
author = {Fernandes, Andrew D and Reid, Jennifer Ns and Macklaim, Jean M and McMurrough, Thomas A and Edgell, David R and Gloor, Gregory B},
title = {Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis},
journal = {Microbiome},
volume = {2},
number = {1},
pages = {1-13},
ISSN = {2049-2618},
year = {2014},
type = {Journal Article}
}
@article{Nearing_Microbiome_2022,
author = {Nearing, Jacob T and Douglas, Gavin M and Hayes, Molly G and MacDonald, Jocelyn and Desai, Dhwani K and Allward, Nicole and Jones, Casey and Wright, Robyn J and Dhanani, Akhilesh S and Comeau, André M},
title = {Microbiome differential abundance methods produce different results across 38 datasets},
journal = {Nature Communications},
volume = {13},
number = {1},
pages = {1-16},
ISSN = {2041-1723},
year = {2022},
type = {Journal Article}
}
@article{Lin_Analysis_2020,
author = {Lin, Huang and Peddada, Shyamal Das},
title = {Analysis of compositions of microbiomes with bias correction},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {1-11},
ISSN = {2041-1723},
year = {2020},
type = {Journal Article}
}
@article{Bewick_Trait_2019,
author = {Bewick, Sharon and Gurarie, Eliezer and Weissman, Jake L and Beattie, Jess and Davati, Cyrus and Flint, Rachel and Thielen, Peter and Breitwieser, Florian and Karig, David and Fagan, William F},
title = {Trait-based analysis of the human skin microbiome},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {1-15},
ISSN = {2049-2618},
year = {2019},
type = {Journal Article}
}
@article{Aßhauer_Tax4Fun_2015,
author = {Aßhauer, Kathrin P and Wemheuer, Bernd and Daniel, Rolf and Meinicke, Peter},
title = {Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data},
journal = {Bioinformatics},
volume = {31},
number = {17},
pages = {2882-2884},
ISSN = {1460-2059},
year = {2015},
type = {Journal Article}
}
@article{Douglas_PICRUSt2_2020,
author = {Douglas, G. M. and Maffei, V. J. and Zaneveld, J. R. and Yurgel, S. N. and Brown, J. R. and Taylor, C. M. and Huttenhower, C. and Langille, M. G. I.},
title = {PICRUSt2 for prediction of metagenome functions},
journal = {Nat Biotechnol},
volume = {38},
number = {6},
pages = {685-688},
DOI = {10.1038/s41587-020-0548-6},
year = {2020},
type = {Journal Article}
}
@article{Peschel_NetCoMi_2021,
author = {Peschel, Stefanie and Müller, Christian L and von Mutius, Erika and Boulesteix, Anne-Laure and Depner, Martin},
title = {NetCoMi: network construction and comparison for microbiome data in R},
journal = {Briefings in Bioinformatics},
volume = {22},
number = {4},
pages = {bbaa290},
DOI = {10.1093/bib/bbaa290},
year = {2021},
type = {Journal Article}
}
@article{Fang_CCLasso_2015,
author = {Fang, Huaying and Huang, Chengcheng and Zhao, Hongyu and Deng, Minghua},
title = {CCLasso: correlation inference for compositional data through Lasso},
journal = {Bioinformatics},
volume = {31},
number = {19},
pages = {3172-318},
ISSN = {1367-4803},
year = {2015},
DOI = {10.1093/bioinformatics/btv349},
type = {Journal Article}
}
@article{Friedman_Inferring_2012,
author = {Friedman, Jonathan and Alm, Eric J},
title = {Inferring correlation networks from genomic survey data},
journal = {PLOS Computational Biology},
volume = {8},
number = {9},
pages = {e1002687},
ISSN = {1553-7358},
year = {2012},
DOI = {10.1371/journal.pcbi.1002687},
type = {Journal Article}
}
@article{Ning_general_2019,
author = {Ning, D. and Deng, Y. and Tiedje, J. M. and Zhou, J.},
title = {A general framework for quantitatively assessing ecological stochasticity},
journal = {Proc Natl Acad Sci U S A},
volume = {116},
number = {34},
pages = {16892-16898},
DOI = {10.1073/pnas.1904623116},
url = {http://www.ncbi.nlm.nih.gov/pubmed/31391302},
year = {2019},
type = {Journal Article}
}
@article{Li_BEEMStatic_2021,
author = {Li, C. and Av-Shalom, T. V. and Tan, J. W. G. and Kwah, J. S. and Chng, K. R. and Nagarajan, N.},
title = {BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data},
journal = {PLoS Comput Biol},
volume = {17},
number = {9},
pages = {e1009343},
DOI = {10.1371/journal.pcbi.1009343},
year = {2021},
type = {Journal Article}
}
@article{Liu_Microbial_2022,
author = {Liu, Chi and Li, Xiangzhen and Mansoldo, Felipe R. P. and An, Jiaxing and Kou, Yongping and Zhang, Xiao and Wang, Junming and Zeng, Jianxiong and Vermelho, Alane B. and Yao, Minjie},
title = {Microbial habitat specificity largely affects microbial co-occurrence patterns and functional profiles in wetland soils},
journal = {Geoderma},
volume = {418},
pages = {115866},
ISSN = {0016-7061},
DOI = {10.1016/j.geoderma.2022.115866},
url = {https://www.sciencedirect.com/science/article/pii/S0016706122001732},
year = {2022},
type = {Journal Article}
}
@article{Zhao_animalcules_2021,
author = {Zhao, Y. and Federico, A. and Faits, T. and Manimaran, S. and Segre, D. and Monti, S. and Johnson, W. E.},
title = {animalcules: interactive microbiome analytics and visualization in R},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {76},
DOI = {10.1186/s40168-021-01013-0},
year = {2021},
type = {Journal Article}
}
@article{McMurdie_Shiny_2015,
author = {McMurdie, Paul J and Holmes, Susan},
title = {Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking},
journal = {Bioinformatics},
volume = {31},
number = {2},
pages = {282-283},
ISSN = {1367-4803},
year = {2015},
type = {Journal Article}
}
@article{Jin_Mian_2021,
author = {Jin, Boyang Tom and Xu, Feng and Ng, Raymond T and Hogg, James C},
title = {Mian: interactive web-based microbiome data table visualization and machine learning platform},
journal = {Bioinformatics},
volume = {38},
number = {4},
pages = {1176-1178},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btab754},
year = {2021},
type = {Journal Article}
}
@article{Kursa_Feature_2010,
author = {Kursa, Miron B and Rudnicki, Witold R},
title = {Feature selection with the Boruta package},
journal = {J Stat Softw},
volume = {36},
number = {11},
pages = {1-13},
year = {2010},
type = {Journal Article}
}
@article{Wilhelm_Predicting_2021,
author = {Wilhelm, Roland C and van Es, Harold M and Buckley, Daniel H},
title = {Predicting measures of soil health using the microbiome and supervised machine learning},
journal = {Soil Biology and Biochemistry},
pages = {108472},
ISSN = {0038-0717},
year = {2021},
type = {Journal Article}
}
@article{Poore_Microbiome_2020,
author = {Poore, Gregory D and Kopylova, Evguenia and Zhu, Qiyun and Carpenter, Carolina and Fraraccio, Serena and Wandro, Stephen and Kosciolek, Tomasz and Janssen, Stefan and Metcalf, Jessica and Song, Se Jin},
title = {Microbiome analyses of blood and tissues suggest cancer diagnostic approach},
journal = {Nature},
volume = {579},
number = {7800},
pages = {567-574},
ISSN = {1476-4687},
year = {2020},
type = {Journal Article}
}
@article{Tu_NCycDB_2018,
author = {Tu, Qichao and Lin, Lu and Cheng, Lei and Deng, Ye and He, Zhili},
title = {NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes},
journal = {Bioinformatics},
volume = {35},
number = {6},
pages = {1040-1048},
abstract = {The nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups and low coverage of N cycle genes and/or gene (sub)families.To solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84 759 and 219 146 representative sequences at 95 and 100% identity cutoffs, respectively. We also identified 1958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to ‘small database’ issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analysis showed that the structure and composition of N cycle gene families were most strongly correlated with latitude and temperature. NCycDB is expected to facilitate N cycle studies via shotgun metagenome sequencing approaches in various environments. The framework developed in this study can be served as a good reference to build similar knowledge-based functional gene databases in various processes and pathways.NCycDB database files are available at https://github.com/qichao1984/NCyc.Supplementary data are available at Bioinformatics online.},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bty741},
url = {https://doi.org/10.1093/bioinformatics/bty741},
year = {2018},
type = {Journal Article}
}
@article{Truong_MeTApHLaN2_2015,
author = {Truong, Duy Tin and Franzosa, Eric A and Tickle, Timothy L and Scholz, Matthias and Weingart, George and Pasolli, Edoardo and Tett, Adrian and Huttenhower, Curtis and Segata, Nicola},
title = {MetaPhlAn2 for enhanced metagenomic taxonomic profiling},
journal = {Nature methods},
volume = {12},
number = {10},
pages = {902-903},
ISSN = {1548-7091},
year = {2015},
type = {Journal Article}
}
@article{Ramette_Multivariate_2007,
author = {Ramette, A.},
title = {Multivariate analyses in microbial ecology},
journal = {FEMS Microbiol Ecol},
volume = {62},
number = {2},
pages = {142-60},
DOI = {10.1111/j.1574-6941.2007.00375.x},
year = {2007},
type = {Journal Article}
}
@article{Anderson_Navigating_2011,
author = {Anderson, M. J. and Crist, T. O. and Chase, J. M. and Vellend, M. and Inouye, B. D. and Freestone, A. L. and Sanders, N. J. and Cornell, H. V. and Comita, L. S. and Davies, K. F. and Harrison, S. P. and Kraft, N. J. and Stegen, J. C. and Swenson, N. G.},
title = {Navigating the multiple meanings of beta diversity: a roadmap for the practicing ecologist},
journal = {Ecology Letters},
volume = {14},
number = {1},
pages = {19-28},
DOI = {10.1111/j.1461-0248.2010.01552.x},
year = {2011},
type = {Journal Article}
}
@article{Tuomisto_diversity_2010,
author = {Tuomisto, Hanna},
title = {A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity},
journal = {Ecography},
volume = {33},
number = {1},
pages = {2-22},
ISSN = {1600-0587},
year = {2010},
type = {Journal Article}
}
@article{Wood_Improved_2019,
author = {Wood, D. E. and Lu, J. and Langmead, B.},
title = {Improved metagenomic analysis with Kraken 2},
journal = {Genome Biol},
volume = {20},
number = {1},
pages = {257},
DOI = {10.1186/s13059-019-1891-0},
year = {2019},
type = {Journal Article}
}
@article{Gibbons_twodynamic_2017,
author = {Gibbons, S. M. and Kearney, S. M. and Smillie, C. S. and Alm, E. J.},
title = {Two dynamic regimes in the human gut microbiome},
journal = {PLoS Comput Biol},
volume = {13},
number = {2},
pages = {e1005364},
DOI = {10.1371/journal.pcbi.1005364},
year = {2017},
type = {Journal Article}
}
@article{Li_expectation_2019,
author = {Li, C. and Chng, K. R. and Kwah, J. S. and Av-Shalom, T. V. and Tucker-Kellogg, L. and Nagarajan, N.},
title = {An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {118},
DOI = {10.1186/s40168-019-0729-z},
year = {2019},
type = {Journal Article}
}
@article{Franzosa_Species_2018,
author = {Franzosa, Eric A. and McIver, Lauren J. and Rahnavard, Gholamali and Thompson, Luke R. and Schirmer, Melanie and Weingart, George and Lipson, Karen Schwarzberg and Knight, Rob and Caporaso, J. Gregory and Segata, Nicola and Huttenhower, Curtis},
title = {Species-level functional profiling of metagenomes and metatranscriptomes},
journal = {Nature Methods},
volume = {15},
number = {11},
pages = {962-968},
ISSN = {1548-7105},
DOI = {10.1038/s41592-018-0176-y},
year = {2018},
type = {Journal Article}
}
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author = {Carpenter, C. M. and Frank, D. N. and Williamson, K. and Arbet, J. and Wagner, B. D. and Kechris, K. and Kroehl, M. E.},
title = {tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R},
journal = {BMC Bioinformatics},
volume = {22},
number = {1},
pages = {41},
DOI = {10.1186/s12859-021-03967-2},
year = {2021},
type = {Journal Article}
}
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author = {Reeder, J. and Huang, M. and Kaminker, J. S. and Paulson, J. N.},
title = {MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities},
journal = {Bioinformatics},
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type = {Journal Article}
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author = {Zhang, X. and Liu, S. and Wang, J. and Huang, Y. and Freedman, Z. and Fu, S. and Liu, K. and Wang, H. and Li, X. and Yao, M. and Liu, X. and Schuler, J.},
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journal = {Nat Commun},
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title = {Large-scale metabolic interaction network of the mouse and human gut microbiota},
journal = {Scientific Data},
volume = {7},
number = {1},
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type = {Journal Article}
}
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author = {Anderson, M. J.},
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title = {R6: Encapsulated Classes with Reference Semantics},
author = {Winston Chang},
year = {2020},
note = {R package version 2.5.0},
url = {https://CRAN.R-project.org/package=R6},
}
@article{Price_theseus_2018,
author = {Price, Jacob R. and Woloszynek, Stephen and Rosen, Gail and Sales, Christopher M.},
title = {theseus - An R package for the analysis and visualization},
journal = {bioRxiv},
DOI = {10.1101/295675},
year = {2018},
type = {Journal Article}
}
@Manual{R-base,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2021},
url = {https://www.R-project.org/},
}
@Manual{R-bookdown,
title = {bookdown: Authoring Books and Technical Documents with R Markdown},
author = {Yihui Xie},
year = {2021},
note = {R package version 0.22},
url = {https://CRAN.R-project.org/package=bookdown},
}
@Manual{R-knitr,
title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
author = {Yihui Xie},
year = {2021},
note = {R package version 1.31},
url = {https://yihui.org/knitr/},
}
@Manual{R-rmarkdown,
title = {rmarkdown: Dynamic Documents for R},
author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
year = {2021},
note = {R package version 2.7},
url = {https://CRAN.R-project.org/package=rmarkdown},
}
@Book{bookdown2016,
title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
author = {Yihui Xie},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2016},
note = {ISBN 978-1138700109},
url = {https://bookdown.org/yihui/bookdown},
}
@Book{knitr2015,
title = {Dynamic Documents with {R} and knitr},
author = {Yihui Xie},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2015},
edition = {2nd},
note = {ISBN 978-1498716963},
url = {https://yihui.org/knitr/},
}
@InCollection{knitr2014,
booktitle = {Implementing Reproducible Computational Research},
editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
author = {Yihui Xie},
publisher = {Chapman and Hall/CRC},
year = {2014},
note = {ISBN 978-1466561595},
url = {http://www.crcpress.com/product/isbn/9781466561595},
}
@Book{rmarkdown2018,
title = {R Markdown: The Definitive Guide},
author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2018},
note = {ISBN 9781138359338},
url = {https://bookdown.org/yihui/rmarkdown},
}
@Book{rmarkdown2020,
title = {R Markdown Cookbook},
author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2020},
note = {ISBN 9780367563837},
url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}
@Manual{R-base,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2016},
url = {https://www.R-project.org/},
}
@Manual{R-bookdown,
title = {bookdown: Authoring Books and Technical Documents with R Markdown},
author = {Yihui Xie},
year = {2016},
note = {R package version 0.3.9},
url = {https://github.com/rstudio/bookdown},
}
@Manual{R-knitr,
title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
author = {Yihui Xie},
year = {2016},
note = {R package version 1.15.1},
url = {https://CRAN.R-project.org/package=knitr},
}
@Manual{R-rmarkdown,
title = {rmarkdown: Dynamic Documents for R},
author = {JJ Allaire and Joe Cheng and Yihui Xie and Jonathan McPherson and Winston Chang and Jeff Allen and Hadley Wickham and Aron Atkins and Rob Hyndman},
year = {2016},
note = {R package version 1.3},
url = {https://CRAN.R-project.org/package=rmarkdown},
}
@article{Theil_rANOMALY_2021,
author = {Theil, S. and Rifa, E.},
title = {rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis},
journal = {F1000Res},
volume = {10},
pages = {7},
DOI = {10.12688/f1000research.27268.1},
url = {http://www.ncbi.nlm.nih.gov/pubmed/33537122},
year = {2021},
type = {Journal Article}
}
@article{Wemheuer_Tax4Fun2_2020,
author = {Wemheuer, Franziska and Taylor, Jessica A. and Daniel, Rolf and Johnston, Emma and Meinicke, Peter and Thomas, Torsten and Wemheuer, Bernd},
title = {Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences},
journal = {Environmental Microbiome},
volume = {15},
number = {1},
ISSN = {2524-6372},
DOI = {10.1186/s40793-020-00358-7},
year = {2020},
type = {Journal Article}
}
@article{Polme_FungalTraits_2020,
author = {Põlme, Sergei and Abarenkov, Kessy and Henrik Nilsson, R. and Lindahl, Björn D. and Clemmensen, Karina Engelbrecht and Kauserud, Havard and Nguyen, Nhu and Kjøller, Rasmus and Bates, Scott T. and Baldrian, Petr and Frøslev, Tobias Guldberg and Adojaan, Kristjan and Vizzini, Alfredo and Suija, Ave and Pfister, Donald and Baral, Hans-Otto and Järv, Helle and Madrid, Hugo and Nordén, Jenni and Liu, Jian-Kui and Pawlowska, Julia and Põldmaa, Kadri and Pärtel, Kadri and Runnel, Kadri and Hansen, Karen and Larsson, Karl-Henrik and Hyde, Kevin David and Sandoval-Denis, Marcelo and Smith, Matthew E. and Toome-Heller, Merje and Wijayawardene, Nalin N. and Menolli, Nelson and Reynolds, Nicole K. and Drenkhan, Rein and Maharachchikumbura, Sajeewa S. N. and Gibertoni, Tatiana B. and Læssøe, Thomas and Davis, William and Tokarev, Yuri and Corrales, Adriana and Soares, Adriene Mayra and Agan, Ahto and Machado, Alexandre Reis and Argüelles-Moyao, Andrés and Detheridge, Andrew and de Meiras-Ottoni, Angelina and Verbeken, Annemieke and Dutta, Arun Kumar and Cui, Bao-Kai and Pradeep, C. K. and Marín, César and Stanton, Daniel and Gohar, Daniyal and Wanasinghe, Dhanushka N. and Otsing, Eveli and Aslani, Farzad and Griffith, Gareth W. and Lumbsch, Thorsten H. and Grossart, Hans-Peter and Masigol, Hossein and Timling, Ina and Hiiesalu, Inga and Oja, Jane and Kupagme, John Y. and Geml, József and Alvarez-Manjarrez, Julieta and Ilves, Kai and Loit, Kaire and Adamson, Kalev and Nara, Kazuhide and Küngas, Kati and Rojas-Jimenez, Keilor and Bitenieks, Krišs and Irinyi, Laszlo and Nagy, László G. and Soonvald, Liina and Zhou, Li-Wei and Wagner, Lysett and Aime, M. Catherine and Öpik, Maarja and Mujica, María Isabel and Metsoja, Martin and Ryberg, Martin and Vasar, Martti and Murata, Masao and Nelsen, Matthew P. and Cleary, Michelle and Samarakoon, Milan C. and Doilom, Mingkwan and Bahram, Mohammad and Hagh-Doust, Niloufar and Dulya, Olesya and Johnston, Peter and Kohout, Petr and Chen, Qian and Tian, Qing and Nandi, Rajasree and Amiri, Rasekh and Perera, Rekhani Hansika and dos Santos Chikowski, Renata and others },
title = {FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles},
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volume = {105},
number = {1},
pages = {1-16},
ISSN = {1878-9129},
DOI = {10.1007/s13225-020-00466-2},
url = {https://doi.org/10.1007/s13225-020-00466-2},
year = {2020},
type = {Journal Article}
}
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year = {2019},
type = {Journal Article}
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type = {Journal Article}
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title = {VennDiagram: Generate High-Resolution Venn and Euler Plots},
author = {Hanbo Chen},
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note = {R package version 1.6.20},
url = {https://CRAN.R-project.org/package=VennDiagram},
}
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DOI = {10.1038/nbt.2676},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23975157},
year = {2013},
type = {Journal Article}
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title = {Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data},
journal = {Cell Systems},
volume = {9},
number = {3},
pages = {286-296 e8},
DOI = {10.1016/j.cels.2019.08.002},
url = {http://www.ncbi.nlm.nih.gov/pubmed/31542415},
year = {2019},
type = {Journal Article}
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title = {Soil bacterial community structure in Chinese wetlands},
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journal = {Scientific Reports},
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@Manual{Jari_vegan_2019,
title = {vegan: Community Ecology Package},
author = {Jari Oksanen and F. Guillaume Blanchet and Michael Friendly and Roeland Kindt and Pierre Legendre and Dan McGlinn and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner},
year = {2019},
note = {R package version 2.5-6},
url = {https://CRAN.R-project.org/package=vegan}
}
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title = {ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}},
author = {E. Paradis and K. Schliep},
journal = {Bioinformatics},
year = {2018},
volume = {35},
pages = {526-528}