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- [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.
- [ ] (optional) I have confirmed this bug exists on the m…
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With valiDrops 0.1.0 in R 4.3.2, x86_64-apple-darwin20, I get this error with one of 12 samples of my snRNA seq. experiment. The sample's data is not of good quality (~150 median features/cell, as aga…
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Hi I am running cpdb_statistical_analysis_method of cellphone db. My anndata shape is (6890, 2000) with following parameters:
```
cpdb_file_path = 'Resources/cellphonedb.zip'
meta_file_pat…
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## Reclustering of summarized data
### Definitions:
* Observations: typically a cell or group of cells
* Features: typically a gene, protein, or group of genes or proteins.
### Assumptions
…
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I have recently been using `scanpy` to analyze my data and get it into a format that I want to share with others. I've been doing that using the Broad's [Single Cell Portal](https://singlecell.broadi…
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Hi,
Thank you for providing such an instresting tool.
I was trying to use custom gene set from TWAS result instead of GWAS result outputted from MAGMA. The code I use to generate .gs file is this:
…
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Listed are the HTAN manuscripts we should curate for cBioPortal:
- [x] -An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer (https://pubmed.ncbi.…
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Thank you for making this data available.
I have stumbled upon an unexpected behavior: for the organ "blood", the cell labels provided do not fit the clusters as seen on a UMAP:
[
![label_umap]…
goepp updated
3 months ago
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Hi, I have a simple question about the example of loading the gene score information prior application:
```
# load adata
adata = sc.read_h5ad("data/expr.h5ad")
# subset gene sets
df_gs = pd.r…
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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 anndata.
- [ ] (o…
Flu09 updated
2 months ago