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-   -   PCoA Plots (http://seqanswers.com/forums/showthread.php?t=74211)

hamcan 02-13-2017 06:57 PM

PCoA Plots
 
Hi Everyone,
I have HiSequencing data that I want to set up PCoA plots for.
These are environmental samples and I want to look at the diversity between the samples in terms of taxonomy.
What programs can I use for PCoA ?
I know R is one option but I have not been able to find a comprehensive tutorial on how to use it.
Thank you

thermophile 02-14-2017 10:17 AM

I recommend Legendre's Numerical Ecology with R for learning how to do multivariate stats in R. Your uni may have it as an ebook

fanli 02-16-2017 09:29 AM

I like the phyloseq R package:
https://joey711.github.io/phyloseq/

If you are new to metagenomics work, you may want to start here:
http://qiime.org/


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