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(high-temp) No 5. Aplha diversity (16S rRNA/ITS) Output

dataset
posted on 07.05.2022, 12:22 by Jarrod ScottJarrod Scott
Output files from the No 5. Aplha diversity Workflow page of the SWELTR high-temp study. In this workflow we used Hill numbers to assess alpha diversity across temperature treatments.

alpha_wf.rdata: contains all variables and phyloseq objects from 16s rRNA and ITS ASV alpha diversity assessment. To see the Objects, in R run load("alpha_wf.rdata", verbose=TRUE)

Additional files:

For convenience, we also include individual phyloseq objects (collected in zip files) where Hill numbers have been added to the sample data tables.

ITS (its_alpha_objects.zip):
its18_ps_work.rds: phyloseq object for the FULL (unfiltered) ITS data.
its18_ps_filt.rds: phyloseq object for the Arbitrary filtered ITS data.
its18_ps_perfect.rds: phyloseq object for the PERfect ITS data.
its18_ps_pime.rds: phyloseq object for the PIME ITS data.

16S rRNA (ssu_alpha_objects.zip):
ssu18_ps_work.rds: phyloseq object for the FULL (unfiltered) 16S rRNA data.
ssu18_ps_filt.rds: phyloseq object for the Arbitrary filtered 16S rRNA data.
ssu18_ps_perfect.rds: phyloseq object for the PERfect 16S rRNA data.
ssu18_ps_pime.rds: phyloseq object for the PIME 16S rRNA data.

Source code for the workflow can be found here:
https://github.com/sweltr/high-temp/blob/master/alpha.Rmd


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