Phyloseq is a fantastic R package that really helped me get started in R. If you need to process your metagenomic data but lack the experience in statistics/R to use, say, the ecology stats R package VEGAN, I highly recommend giving Phyloseq a try. Running through the vignettes will produce great heatmaps, taxonomy plots, and PCA/NMDS plots.
As I became more comfortable in R, I found myself relying on Phyloseq less and using the VEGAN packages Phyloseq was wrapping more. Still, Phyloseq is a fantastic stepping stone for scientists studying metagenomics who are not ecologists themselves.
I’ll be posting some solutions to problems I’ve encountered working with my own data over the next few months.
Official Phyloseq publication: DOI: 10.1371/journal.pone.0061217