See the pkdown site here.
Biological studies, especially in ecology, health sciences and taxonomy, need to describe the biological composition of samples. During the last twenty years, (i) the development of DNA sequencing, (ii) reference databases, (iii) high-throughput sequencing (HTS), and (iv) bioinformatics resources have allowed the description of biological communities through metabarcoding. Metabarcoding involves the sequencing of millions (meta-) of short regions of specific DNA (-barcoding, Valentini, Pompanon, and Taberlet (2009)) often from environmental samples (eDNA, Taberlet et al. (2012)) such as human stomach contents, lake water, soil and air.
MiscMetabar aims to facilitate the description, transformation, exploration and reproducibility of metabarcoding analysis using R. The development of MiscMetabar relies heavily on the R packages dada2, phyloseq and targets.
Installation
There is no CRAN or bioconductor version of MiscMetabar for now (work in progress).
You can install the stable version from GitHub with:
install.packages("devtools")
devtools::install_github("adrientaudiere/MiscMetabar")You can install the developement version from GitHub with:
install.packages("devtools")
devtools::install_github("adrientaudiere/MiscMetabar", ref = "dev")Some use of MiscMetabar
See vignettes in the MiscMetabar website for more examples.
Summarize a physeq object
library("MiscMetabar")
library("phyloseq")
library("magrittr")
data("data_fungi")
summary_plot_pq(data_fungi)
Alpha-diversity analysis
p <- MiscMetabar::hill_pq(data_fungi, variable = "Height")
#> Taxa are now in rows.
#> Cleaning suppress 0 taxa and 0 samples.
p$plot_Hill_0
Hill number 1
p$plot_tuckey
Result of the Tuckey post-hoc test
Beta-diversity analysis
ggvenn_pq(data_fungi, fact = "Height") +
ggplot2::scale_fill_distiller(palette = "BuPu", direction = 1) +
labs(title = "Share number of ASV among Height in tree")
Installation of other softwares for debian Linux distributions
vsearch
sudo apt-get install vsearch