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@visead reports:
`Both of the following examples should return results, but don't. The connection between taxonomy and dating appears to be broken`
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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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This is a new warning being generated by the tests, and I don't think there are actually should be collinear variables here so I'm not sure what's happening.
``` r
suppressPackageStartupMessages(l…
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Problem description
As in title, this report is forward from https://github.com/nf-core/taxprofiler/issu…
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Hi all,
I have a phyloseq object and I would like to know and then plot the 10 most abundant taxa at family level for each species.
To give you a better idea of my data, I have the relative abu…
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I wanted to plot abundances using centered log ratio, so I did the transformation. Then, I needed to agglomerate my taxa by some specific taxonomic level, e.g. Phylum, and after that I psmelt-ed the r…
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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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Label-free quantification
Label-free quantification is a method that aims to determine the relative amount of proteins in two or more biological samples. It may be based on precursor signal intensity…
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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…