In cdsanchez18/EcoPLOT: EcoPLOT: dynamic and interactive analysis of multivariate biogeochemical datasets

Citations

EcoPLOT is constructed from a novel combination of existing R packages. The EcoPLOT development team would like to recognize the following packages for their contributions.

Dean Attali (2020). shinyjs: Easily Improve the User Experience of Your Shiny Apps in Seconds. R package version 2.0.0. https://CRAN.R-project.org/package=shinyjs

Emmanuel-Lin Toulemonde (2020). dataPreparation: Automated Data Preparation. R package version 1.0.1. https://CRAN.R-project.org/package=dataPreparation

Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes. R package version 1.1-2. https://CRAN.R-project.org/package=RColorBrewer

Garrett Grolemund, Hadley Wickham (2011). Dates and Times Made Easy with lubridate. Journal of Statistical Software, 40(3), 1-25. URL https://www.jstatsoft.org/v40/i03/.

Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194

Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2021). dplyr: A Grammar of Data Manipulation. R package version 1.0.7. https://CRAN.R-project.org/package=dplyr

H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.

Hadley Wickham and Jennifer Bryan (2019). readxl: Read Excel Files. R package version 1.3.1. https://CRAN.R-project.org/package=readxl

Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20. URL http://www.jstatsoft.org/v21/i12/.

Hadley Wickham (2019). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.4.0. https://CRAN.R-project.org/package=stringr

Hadley Wickham (2021). tidyr: Tidy Messy Data. R package version 1.1.3. https://CRAN.R-project.org/package=tidyr

Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs and Helene Wagner (2020). vegan: Community Ecology Package. R package version 2.5-7. https://CRAN.R-project.org/package=vegan

Joe Cheng, Carson Sievert, Barret Schloerke, Winston Chang, Yihui Xie and Jeff Allen (2021). htmltools: Tools for HTML. R package version 0.5.2. https://CRAN.R-project.org/package=htmltools

LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution 2020, 37(2):599-603. doi: 10.1093/molbev/msz240

Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 (2014)

Microsoft Corporation and Steve Weston (2020). doParallel: Foreach Parallel Adaptor for the 'parallel' Package. R package version 1.0.16. https://CRAN.R-project.org/package=doParallel

Orchestrating high-throughput genomic analysis with Bioconductor. W. Huber, V.J. Carey, R. Gentleman, ..., M. Morgan Nature Methods, 2015:12, 115.

phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. Paul J. McMurdie and Susan Holmes (2013) PLoS ONE 8(4):e61217.

qiime2R: Importing QIIME2 artifacts and associated data into R sessions. Jordan E Bisanz (2018) https://github.com/jbisanz/qiime2R.

Sumanta Basu and Karl Kumbier (2018). iRF: Iterative Random Forests. R package version 3.0.0.

Winston Chang (2021). shinythemes: Themes for Shiny. R package version 1.2.0. https://CRAN.R-project.org/package=shinythemes

Winston Chang, Joe Cheng, JJ Allaire, Carson Sievert, Barret Schloerke, Yihui Xie, Jeff Allen, Jonathan McPherson, Alan Dipert and Barbara Borges (2021). shiny: Web Application Framework for R. R package version 1.6.0. https://CRAN.R-project.org/package=shiny

Yihui Xie, Joe Cheng and Xianying Tan (2021). DT: A Wrapper of the JavaScript Library 'DataTables'. R package version 0.18. https://CRAN.R-project.org/package=DT

cdsanchez18/EcoPLOT documentation built on Feb. 21, 2022, 2:08 p.m.