R package for Taxonomy Analysis and ...

Other Bioinformatics Tools
1

Hello all,
Can I analyze alpha and beta diversities, taxonomy analysis of biom file (OTUs table), and PCoA, heatmap, and more with a R package? If yes, could you please introduce me that?
Thanks,
Qiimer

2

Hi Qiimer,

Yeah, there's some great packages out there. I use phyloseq (phyloseq: Explore microbiome profiles using R). I think there is also a community tutorial within the qiime2 docs about performing data analysis in R, which probably contains great suggestions on other packages also (Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R). I haven't used qiime2r (sounds pretty great!), but I know that phyloseq allows you to import and work with .biom tables.

Hope that helps!

Mark

2 Likes
3

Dear Mark,

Thanks for the answer. I have tried to install Qiime2R in R, but it needed some packages prior to installing Qiime2R. I installed some like biomanager and devtools, but another one is ps that I could not install it. It gives an error is below:

ERROR: failed to lock directory 'D:/Program Files/R/R-4.0.2/library' for modifying
Try removing 'D:/Program Files/R/R-4.0.2/library/00LOCK-ps'
Warning in install.packages :
installation of package ‘ps’ had non-zero exit status

Thanks for the suggestion.
Qiimer