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
There is no CRAN or bioconductor version of MiscMetabar for now (work in progress).
You can install the stable version from GitHub with:
You can install the developement version from GitHub with:
install.packages("devtools") devtools::install_github("adrientaudiere/MiscMetabar", ref = "dev")
See vignettes in the MiscMetabar website for more examples.
library("MiscMetabar") library("phyloseq") library("magrittr") data("data_fungi") summary_plot_pq(data_fungi)
p <- MiscMetabar::hill_pq(data_fungi, variable = "Height") #> Taxa are now in rows. #> Cleaning suppress 0 taxa and 0 samples. p$plot_Hill_0
ggvenn_pq(data_fungi, fact = "Height") + ggplot2::scale_fill_distiller(palette = "BuPu", direction = 1) + labs(title = "Share number of ASV among Height in tree")
sudo apt-get install vsearch