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While submitting #904, I was looking at this bit of the code in ``biom/parse.py`` function ``parse_uc`` (Create a Table object from a uclust/usearch/vsearch uc file):
https://github.com/biocore/bio…
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This produces a simple 4 sample, 10 observation test case with all observations having metadata for headers, shoulders, knees and toes (non-alphabetical order as per the song), and all samples having …
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Hi @mortonjt ,
I hope all is well!
I am having trouble running the standalone version of Songbird. Please see below my code and the error message I am getting.
Would love to hear your thou…
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I have a [bioconda package](https://github.com/bioconda/bioconda-recipes/pull/39809) that depends on biom-format. Among its tests is a `pip check` which reports cython as missing.
I see two possibl…
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Hi, it's a really easy bug to reproduce, just the mdk without any tweaks with the addition of any datagen, execute the runData task, you will get this :
https://gist.github.com/drkhodakarami/c19d20f…
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Hi Vova,
@LisaHuelsmann alerted me to the fact that the current calibration code in the vignette does not result in a good calibration, for whatever reason. In the vignette, we currently load MCMC …
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Hi,
I tried to load phyloseq object.
```R
library(ampvis2)
otutable
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Hi there,
I have my OTU tables in just .txt, .xlsx, or .csv format. I see that Songbird requires a .biom format. Are there any ways to work around this? Thank you
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### Description of feature
We should consider standardising how output tables should look like.
This could be done with simple parsing and production of (standardised, if possible) `TSV` tables,…
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Example [analysis MGYA00199483](https://www.ebi.ac.uk/metagenomics/analyses/MGYA00199483), assuming these are the files required:
| reads | name | format | url |
| --- | --- | --- | --- |
| Taxon…