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I tried to run the tutorial and found out the google drive link to pbmc.h5ad is no longer working.
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Hi, I was interested to look further into the Spatial Transcriptomics datasets from 3 patient-derived GBM samples that was recently published last week in Nature Communication. However, I am running i…
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Talking to @fbastian
- They have an RDF dump and also JSON but it may be fine to keep using TSV although we may need to switch to their H5AD
- they have someone actively working on improving th…
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Dear Author,
I am using this script for analysis:
import SEVtras
SEVtras.sEV_recognizer(input_path='/home/yeziyang/Sc', sample_file='/home/yeziyang/Sc/Sc1_LN', out_path='/home/yeziyang/Sc/outputs…
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Here is a minimal code example that shows the unexpected behavior.
First, let's make the `ad` object and inspect the dtypes:
```python
import anndata
import zarr
from scipy import sparse
imp…
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Having extra metadata you can add to denote the interface of an h5ad and h5mu file can be used later on for checking whether the files adhere to a certain interface.
Right now a viash config doesn'…
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Hi,
I tried both the conda and docker (using singularity) versions
I run the following
MATK -t SuperCell -i data/cd34_multiome_rna.h5ad -o MATK_output/SuperCell/cd34/ -n 50 -f 2000 -k 30 -g 75…
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Hi all,
Besca contains references to some LFS files. As far as I understand, when someone git clones the repo, LFS files are also pulled.
We currently are over bandwidth, which means that none o…
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Since Python 3.7 dictionaries [are ordered](https://stackoverflow.com/a/39537308/2340703).
Anndata does not preserve the order of dictionaries when saving and reloading, but reorders them alphabet…
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Currently, we use presto for Seurat and SCE to implement quick wilcoxon rank sum DE testing and auROC calculation, but presto doesn't support DelayedArray or BPCells sparse matrices (and won't support…