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Operational Taxonomic Units (or OTUs) will be mostly analyzed with their profiles (counts or transformed counts). Two models (tables) will store information associated with OTU profiles:
* OTUProfile…
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Hi, first of all I want to say thanks for developing such a cool tool for analyzing microbiome data! It is super helpful.
I am currently having issues with the top_taxa function. I have a phyloseq …
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Hi,
I have been running simper without problems
simper(fourth_root_sqrt_OTU_abundances_relative, AGDX_samples$Fjord, permutations=1000)
However, when I tried to repeat the analysis with simper.…
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Looking at Visumap, the majority of those algorithms are found in scikit-learn or scikit-bio, namely
**Ordination**
- [SMACOF](https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/manifol…
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Hi,
I'm trying to use glmmseq to analyze some dataset in which each patient contributed multiple samples. I want to consider patient ID as random factor and the diagnosis as fixed factor. So my for…
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Hi, when I am running **plot_diff_cladogram**, an strange error occured.
"""
Select 50 significant features ...
Provided use_taxa_num: 200 >= total effective taxa number. Skip the selection ...
…
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net_hv_spiceasi
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Hi,
I'm trying to use fantaxtic to get the top 10 most abundant genera across a complete phyloseq object and list the relative abundances of these top genera. I was trying to do this like so:
`…
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The function `loadFromBiom` has outdated example section:
- refers to `se` (not `tse`) as function output, although the function seems to return TreeSE
- converts SE to TreeSE although the object …
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Hi，
There are 8 columns, and the first column is the OTU number that I manually set. The second to seventh columns are the sample names. The last column is species classification.
And I h…