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I recently started dipping my toes into published datasets from the Oxford Nanopore MinION sequencer. Their format is an hdf5 file, containing several types of metadata, "event data" (which is essenti…
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I am trying to run qiime2 through jupyterLab terminal in a mac for the first time, and I am getting this error.
zsh: no matches found: SampleData[PairedEndSequencesWithQuality]
zsh: command not fou…
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* link to support ticket: [2024062660000426](https://otrsdict.ugent.be/otrs/index.pl?Action=AgentTicketZoom;TicketID=160460;ArticleID=563062)
* website: https://biom-format.org
* installation docs: …
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Something like `biom filter-blanks -i foo -o bar`, where any sample containing "blank" case insensitive is dropped
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Hi Folks,
I was wondering is it possible to use ktImportText on multiple samples in just one text file?
I have a text file containing multiple samples (actually 20) with taxonomy classification an…
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**First of all, I absolutely love this! Great job, honestly.**
Are there currently any plans regarding 1.17 compatibility?
If so, how long after the release of 1.17 would you estimate this mod w…
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Hello, I tried to transfer dataframe to a biom Table using the skbio.table.Table. However, I got 'biom.exception.TableException: Duplicate observation IDs' error even I already removed potential dupli…
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This table:
``` python
> t.metadata()
Out[5]:
(defaultdict(, {u'pH': 7.0}),
defaultdict(, {u'pH': 8.0}),
defaultdict(, {u'pH': 7.0}),
defaultdict(, {}))
```
Will cause `to_hdf5` to except. It is …
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Handling sparse abundance matrices is tricky because one of the
first steps is to center it, which destroys sparsity. On the other
hand, it could be helpful to use scipy.sparse.svds instead of
np.lina…
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Hi, I imported my files from qiime2 into a phyloseq object:
physeq1