speedyseq – Enhanced phyloseq Functions

I recently discovered the R package speedyseq by Michael McLaren. It includes much faster implementations of some phyloseq functions : tax_glom(), tip_glom(), and the plotting functions that make use of psmelt()plot_bar(), plot_heatmap(), and plot_tree(). There are also lots of convenience functions including ones for extracting the otu, sample data and taxonomy tables, and even the entire phyloseq object, as tibbles.

For further information, check out the Readme file on GitHub at https://github.com/mikemc/speedyseq.

speedyseq can be installed in R using either of the following methods:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("mikemc/speedyseq")

Or:

if (!requireNamespace("devtools", quietly =TRUE))
    install.packages("devtools")
devtools::install_github("mikemc/speedyseq"

 

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