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I don't know why but phyloseq allows two kind of otu layout in a phyloseq object; one is taxa_are_row and the other one not. To access this information, one can use taxa_are_row(phyobj) to check.
W…
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Hello,
I am excited to use the MicrobioStat package in order to test for differences in alpha diversity accross timepoints.
I have been working with phyloseq object so far and I would like to con…
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Hi!
I tried PIME package using this pipeline:
```
pime.oob.error(phyloseq, "phenotype")
phy_BrDi
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Hi,
I'm finding as the title. The seqtab object has 75 samples and the phyloseq object has 69.
The code is pretty simple:
`fitGTR
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Hi Joey,
In post #508 above you wrote:
## How To Merge
The OTU IDs between the studies need to match up. You can use **merge_taxa** to get around this, but this is meaningful only if the taxon…
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It works quite nicely. I will probably build additional functionality based on the same approach. The current capabilities are documented in-package (where I attribute your contribution and provide a …
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Hello,
I'd like to install the phyloseq package for R using conda. I just installed R through conda.
Conda can't find the specific package from 'https://anaconda.org/bioconda/bioconductor-phyloseq'.…
kpitz updated
7 years ago
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Using the Phyloseq object, after run_lefse, plot_ef_bar was normally derived.
However, plot_cladogram or microbiomeMarker::plot_cladogram
causes the following problem:
command
microbiomeMarker…
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Thanks for contributing these phyloseq tools.
I'm wondering if we could integrate these tools into the IUC repository: https://github.com/galaxyproject/tools-iuc/blob/master/tools/phyloseq/?
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Hi,
Would you mind to answer me the two questions from me?
1. After I follow your scripts: how to convert phyloseq object to mpse?
#convert phyloseq object to mpse
#library(phyloseq)
#data(es…