FUNGuild importing Data - Michael-D-Preston/PrestonLab GitHub Wiki

By Angus Ball

NOTE: THIS PAGE IS DEPRECATED PLEASE USE FungalTraits importing Data, its a better database

Introduction

FUNGuild is a program that attaches metabolism information to the taxons of fungi produced by metabarcoding. To use the below tutorial you are expected to have finished the DADA2 pipeline, but have yet to create a phyloseq object, BUT because I'm lazy I don't explain the phyloseq code within this documentation, see Making-a-Phyloseq-Object to understand what the phyloseq code is doing

Link

FUNGuild importing data

Citations

Citations in R are hard, here are all the packages you use and how to cite them, but you don't necessarily need to cite all of them? Depends on the ethical considerations regarding data management packages (always cite statistical packages). For this section please cite:

FUNGuild

Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, Schilling JS, Kennedy PG. 2016. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology 20:241–248.

Phyloseq:

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.

ggplot:

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

janitor:

Firke S (2023). janitor: Simple Tools for Examining and Cleaning Dirty Data. R package version 2.2.0, https://CRAN.R-project.org/package=janitor.

dplyr:

Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.3, https://CRAN.R-project.org/package=dplyr.

tidyverse:

Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). “Welcome to the tidyverse.” Journal of Open Source Software, 4(43), 1686. doi:10.21105/joss.01686 https://doi.org/10.21105/joss.01686.

ggpubr:

Kassambara A (2023). ggpubr: 'ggplot2' Based Publication Ready Plots. R package version 0.6.0, https://CRAN.R-project.org/package=ggpubr.

ape:

Paradis E, Schliep K (2019). “ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.” Bioinformatics, 35, 526-528. doi:10.1093/bioinformatics/bty633 https://doi.org/10.1093/bioinformatics/bty633.

splitstackshape: