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The regular read_10x_h5() function neglects the gRNA in scRNA-seq CRISPR data which were provided to cell ranger (does not show In adata.X and adata.var). However, with the read_mtx() it is included i…
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Hi Robrecht, I encountered this problem when trying to load one of the example datasets using `read_h5ad(..., backed = "r")`:
``` r
library(anndata)
example var: 'gene_ids', 'feature_types…
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Hey there,
Found out today (from [a question on discourse](https://discourse.scverse.org/t/add-title-to-scanpy-pl-heatmap/644)) that some plotting documentation is misleading. The ['return' section](…
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Hi,
I used Seurat and BPcells to analyze my data. When I used the following code and try to SaveSeuratRds, a waring occured:
```
> sce SaveSeuratRds(sce,"./integrate/process_data/sce_total_rm_…
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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.
- [x] (option…
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`rank_genes_groups` “returns” two recarrays, each with the shape #cells×#groups. one of them stores gene IDs, one the genes’ scores.
the problem with this is that recarrays store their column index…
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**Describe the bug**
Just installed cellxgene, and tried to load a dataset of mine, got this error and fails to load.
**Version (please complete the following information):**
- Desktop or hoste…
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Hello all,
thanks for the great package.
I am having issues running the aucell part of your tutorial more specifically line 45:
!pyscenic aucell \
{f_loom_path_scenic} \
reg.csv \
…
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Hello! Would it be possible to allow other things inside `{}` instead of erroring out? https://myst-parser.readthedocs.io/en/latest/syntax/typography.html uses these for various directives. At the …
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Hello!
I am having trouble calling peaks with MACS3 using `snap.tl.macs3()`. The issue I have is very similar—or related to—this https://github.com/kaizhang/SnapATAC2/issues/336. In my case, I beli…