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For the alpha diversity metrics, the ability to disable validation is only sometimes present. For beta diversity, if using metrics from SciPy directly (not through `skbio.diversity.beta_diversity`) va…
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**Is your feature request related to a problem? Please describe.**
It would be great if phylogenetic beta diversity was accessible via a script so it could be called from the command line.
**Descr…
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Hello,
I used a mantel test on centered environmental data and the Bray-Curtis distances of the microbial community data. My first question is if the environmental data is used to create a Euclide…
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AFAIK, the documentation requested by the author of [this post](https://groups.google.com/forum/#!topic/qiime-forum/K2Bufi7qhas) on the QIIME forum does not exist.
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beta_diversity.py has two input methods: (1) one single input file, and (2) an input folder. The issue is that in both cases it outputs a folder, which can be annoying. Can we make it: (1) one single …
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This script has two steps that are not need it:
beta_diversity.py
upgma_cluster.py
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Hi,
I have a question about Mantel test and Pearson's correlation.
I have a taxonomic profile of soil samples, I have calculated the alpha and beta diversity using Microeco. Then I ran a differe…
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Hi, thanks for building and maintaining this fantastic package.
I am wanting to use the DESeq2 method in your trans_diff function but come across the following error:
` t1 293 input features ..…
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The documentation for `get_beta_diversity_metrics` suggests it should return all valid beta div metrics for skbio, but it only returns two.
```python
>>> skbio.diversity.get_beta_diversity_metrics…
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