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When using the covert function I get the following error using the Villani dataset from https://www.covid19cellatlas.org/:
Error: Not a sparse matrix
It generates a file output but then LoadH5Seu…
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Hello!
I was wondering if there is any way to extract loadings for Palantir diffusion components to determine which genes contribute most to a specific component. Essentially like scanpy and seurat…
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## Description
...
## Minimal reproducible example
```python
import numpy as np
import scanpy as sc
import squidpy as sq
sc.logging.print_header()
print(f"squidpy=={sq.__vers…
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### Please make sure these conditions are met
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of scanpy.
- [ ] (option…
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I plot heatmap for normalized gene expression for 34 clusters. The code is as below:
sc.pl.heatmap(adata, marker_genes, use_raw=False, swap_axes=True, show=False, show_gene_labels=True, save=ofile…
jhu99 updated
3 years ago
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**Describe the bug**
'ir.tl.chain_qc' states that it should mark cells that don't have any detected immune receptor (as stated in the docs). In the new data structures, this information should be in…
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I'm trying to run the scGCO pipeline and the execution seems stuck when I start running `identify_spatial_genes`.
Running ubuntu 20.04 on wsl2. I also needed to change some functions as some of the…
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Taken from @lazappi great list of TODOs in his PR with some additions of mine:
Todo:
- [ ] Decide on the "batch correction"/"data integration" terminology
- [ ] Update the methods figure
- […
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Dear Dr Zheng,
Thank you for providing MEBOCOST. When using "mebo_obj.infer_commu" function, i found one error below.
commu_res = mebo_obj.infer_commu(
n_shuffle=1000,
seed=12345,
Return=True,…
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I'm having issues converting **scipy** matrices (possibly other things as well but this is the reproducible example).
```python
import anndata2ri
from rpy2.robjects import globalenv
from rpy2.ro…