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Questions tagged [phyloseq]

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I want to know what are the main differences between two R Objects constructed for analysis of microbiome data: phyloseq and TreeSummarizedExperiment

I am looking for main differences between two R Objects constructed for analysis of microbiome data: phyloseq object and TreeSummarizedExperiment object First, I will provide a little information ...
akspat's user avatar
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2 votes
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otu_table from phyloseq object does not have correct abundance: all asv are "0" for specific group of samples

This question was also asked on stack overflow I have QIIME2 outputs (feature table, tree, taxonomy, and metadata) that I've imported into R using qiime2R (v. 0.99.6) ‘qza_to_phyloseq’ to create a ...
Geomicro's user avatar
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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 ...
77__bio's user avatar
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-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 ...
gabt's user avatar
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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 : ...
Gaël.T's user avatar
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1 answer
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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 ...
bioinfonext's user avatar
1 vote
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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 ...
bioinfonext's user avatar