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Old 02-13-2017, 06:57 PM   #1
hamcan
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Location: Toronto

Join Date: Nov 2016
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Default 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
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Old 02-14-2017, 10:17 AM   #2
thermophile
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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
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Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
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Old 02-16-2017, 09:29 AM   #3
fanli
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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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