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With large Anndata objects, I sometimes want check the attributes present. The print/repr call does this okay, but becomes hard to read with highly populated objects and not possible to compared two o…
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**Describe the bug**
Can't save h5mu from Scirpy processed gex+bcr+tcr data if I copy airr into obs (i.e. `tdata.obs = tdata.obs.join(ir.get.airr(tdata, tdata.obsm['airr'].fields))`).
Unlike in #4…
Ngort updated
2 months ago
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We would like to expose an API for working with completley backed `AnnData` (and `MuData`) objects.
# Current state
Currently we only expose limited functionality for this, `backed` mode, `AnnLo…
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I am currently using the SCENIC+ pipeline, and I've encountered an issue where several expected outputs are missing from the results. Specifically, the following outputs are not being generated:
AUC…
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Hello,
I'm using the development version of SCENIC+.
When running the snakemake pipeline, it seems to get stuck on 'download_genome_annotations'...
Contents of my Snakemake folder:
-rw-r…
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This issue is to collect ideas that can be tackled during a Hackathon. This could be a both a fully-fletched hackathon event with 10s of participants from the entire community, or a small, informal ga…
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# train model
blast = cb.blast.BLAST(models, train) #.build_empirical()
# this work well，but when I interpret it return error
test_pred = blast.query(test)
[INFO] Cell BLAST: Projecting to latent …
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**Describe the bug**
upon loading scirpy I get the following error message.
ModuleNotFoundError: No module named 'Levenshtein'
checking for levenstein, resulted in it to be present:
python-levenshtein…
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I think it would be useful to add a datasets module. It's very useful for prototyping and debugging.
For prototyping, you've always got a couple extra objects to try a function on. This is also gre…
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As suggested by @grst on Slack: "Once we have cellranger, it should also support (10x) cite-seq out-of-the-box. IDK how difficult it would be to support this with the other aligners."
It appears th…