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@wdwvt1 has existing code for making more basic rarefaction plots that scale better to current datasets. Will put that in place by gutting current `make_rarefaction_plots.py` and replacing with his co…
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One should be present at the base of the repository
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The following changes need to be made to normalize_table.py prior to the 1.9.0 release:
- [x] script description says to test for OTU correlation, but script output description says _not_ to do this. …
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The metric is producing distance matrices in which the diagonal is not assured to be zero'd. This violates the hollow requirement of the skbio `DissimilarityMatrix`.
Should all methods from beta div…
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trying to install a fresh installation (in a virtual environment) using `pip install git+git://github.com/qiime/qiime.git` got the following error:
```
Could not find a version that satisfies the req…
ghost updated
9 years ago
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Not immediately sure how best to improve this. While working on an issue with @ElDeveloper, @wasade, and @antgonza, noticed that loading all metadata (basically [these lines](https://github.com/bioco…
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Hi,
I used the biom-format python package to elaborate a biom.Table (obtained in QIIME) and, following the tutorial, collapse it at the phylum level by doing the following:
```
from biom import load_…
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Joey and Michelle,
Thanks again for all the suggestions!
I went through the examples with GlobalPatterns and everything turned out fine. I am using the import_biom function two things are coming …
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`biom convert -i TEST.biom -o xyz.txt --to-tsv --table-type='OTU table'` and
`biom convert -i test.biom -o xyz.txt --to-tsv --table-type='OTU table'` both work, regardless of the case of of `TEST.bio…
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