Questions tagged [phyloseq]

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Filter phyloseq sequence table

I have phyloseq object where sequence table were builded by using the function mergeSequenceTables from DADA2 package, to merge ten sequence tables from different runs. The sample_data consist of two ...
  • 21
-1 votes
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Translating Simpson and Shannon diversity indices?

So I am trying to compute diversity indices for a dataset I have but the math doesn't work out and I don't really understand how to translate Shannon and/or Simpson diversity indices into something ...
  • 320
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How to create Beta Diversity distance boxplot

I'm trying to generate boxplot from Beta diversity boxplot between two conditions from a phyloseq object. I have a Morisita-horn distance generated by vegdist fonction : ...
  • 21
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1 answer

Regarding canonical analysis of principal coordinates (CAP) for linking microbial data with elements

I used the below code to do CAP analysis to link microbial data with elements, but not sure how to do statistical analysis to show which element variation is responsible most for the difference in ...
1 vote
1 answer

Confirmation about PERMANOVA and Variance partitioning (permutest)

Could you please help me to understand what is the difference between Permutational multivariate analysis of variance (PERMANOVA,adonis) and Variance partitioning (permutest). I understood that ...