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Hi,
I tried to use tax_glom to extract the genus level phyloseq of a complete phyloseq object. And I accidently found that the abundances of the genus after tax_glom were doubled. Would you know w…
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Hi,
I would have a question regarding the use of tax_glom and rarefy_even_depth in phyloseq.
For my study, after having merged the tree, the metadata, the OTU table and taxonomy, I first used tax_…
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Hi,
I am currently running `coverm genome` to estimate the abundance of multiple viral genomes in my samples. However I am not sure which is the best way to do this:
- Is it correct to specify w…
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Hi,
I would like to create some barplots with calculated values of an absolute abundance.
I have a Phyloseq object with relative abundance values, created like this from a standard count table of il…
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Shouldn't the top taxa (genus level here) should be the same output for the RA stacked bar chart of relative abudances (RA) above certain threshold?
I used the same inputs for either of them and I …
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Thank you for creating an excellent program. In the MW-score_result_table_input file there is a column that has the coverage value average. I am assuming that this can be used as relative abundance fo…
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Is there a way to format the data for metamicrobiomeR starting from a phyloseq object?
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Thanks of the great tool!
Regarding the prevalence method, do I get it right that it only considers the presence/absence of an ASV (etc) in samples and controls (rather than prevalences within eac…
mniku updated
5 years ago
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Hi Joey,
I am having trouble filtering my otu table and I hope you could help me with it.
I want to filter to keep only OUTs which is >1% or relative abundance in any of the samples (it might be
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Hi Zach,
I have a shotgun metagenomic sequencing dataset consisting of 17 patients that have daily vaginal microbiome samples for a period of 21 days post surgical obstetric fistula repair, and I wan…