Analyze my QIIME results with Rstudio

[KatherinePena (Katherine Peña Valencia)]

Hi all, I am new to the topic of microbiome analysis and using QIIME. Use Qiime to perform the Taxonomic Bar Plots and the alpha and beta diversity indices. I would like to know what file I can use in Rstudio to be able to replicate the graphics that I obtained in qiime. Should I use the qza file? Or should I convert the qza file to a specific format? I need graphics that can be used in my article.

I Appreciate your help.

Thanks,

[colinbrislawn (Colin J Brislawn)]

Hello @KatherinePena,

Welcome to the forums!

Qiime2 and RStudio are pretty different pieces of software, but they work well together!

I would start here:

Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R

Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R (March 2020 Update v0.99.20) Background The qiime artifact is a method for storing the input and outputs for QIIME2 along with associated metadata and provenance information about how the object was formed. This method of storing objects has a number of obvious advantages; however, on the surface it does not lend itself to easy import to R for the R-minded data scientist. In reality, the .qza file is a compres…

That's a great way to get .qza files from Qiime2 into R, and then you can use the R packages you like best.

-> R

[KatherinePena (Katherine Peña Valencia)]

Hi @colinbrislawn Thank you so much for your reply.

I will try the tutorial you recommend.

I hope I can get the desired results.

Best.