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Hello-
We're publishing some data as MuData in the HuBMAP consortium, and we're also planning to use it to store descriptions and annotations of objects in segmentation masks.
These descriptions…
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This is the current implementation of writing metadata in JSON format for ingest into HuBMAP infrastructure:
```python
def extract_metadata_write_json(mdata: mudata.MuData, output_json: Path):
…
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**Is your feature request related to a problem? Please describe.**
Reading and writing MuData is a bit slow sometimes. For example, after doing some TCR sequence analyses the MuData takes longer to r…
racng updated
5 months ago
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Hello,
Thanks for developing this package. I have been following the Liana+ tutorial, and came across an import error after installing liana package. The python version is 3.9.
#import liana
im…
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**Describe the bug**
mudata v.0.2.3 version, anndata v0.9.2, calling mudata.update(), causing anadata data update failure, confirming that there are no duplicate data in the original data, generating…
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https://mudata.readthedocs.io/en/latest/api/generated/mudata.read.html
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We should have a nicer repr for the anndata object. Ideally a rich one with more info and collapsibility. [`mudata` already has this implemented](https://muon.readthedocs.io/en/latest/notebooks/quicks…
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Use the Mudata from https://github.com/IGVF-CRISPR/Pipeline_Gasperini_2019/tree/main/mudata
to return a cell x guide binary matrix corresponding to the guide presence.
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Mostly FYI:
I noticed that the community behind `scanpy` and `anndata` (which was used as the backend data model for `omicser`) have formed the scverse: https://scverse.org/packages/#ecosystem
It lo…
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"You may download a preprocessed 10X Multiome demo dataset [here](https://figshare.com/s/b0840d90e42e37fa165f)."
The link downloads RNA_ATAC_PBMC_demo.h5mu.gz
However, when I try to gunzip this fi…