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Currently, we are experiencing extreme overrepresentation of Hypendymal cells after running InSituType.
It seems to be the go-to celltype when the data is shallow. Although the data has passed QC me…
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Extend the function class so that it can efficiently handle different celltypes.
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Can I define new celltype using xCell with a list of genes?
For example, define TRM cells with "CD8A, CD69, CD103, PDCD1 and TOP2A"
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Hi,
I've been using `scimilarity` to annotate cells in multiple different datasets. As a sanity check, I ran `scimilarity` on cells for which I already had cell type annotations performed with ano…
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Hi, the documentation for your DEG function states "Differential expressed genes will
be called within each cell type by the method users select." However, when I run it with data that has more …
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Hi, I was wondering if it is possible to extract downregulated genes if I am analyzing communication between cellA and cellB?
Apparently, the function subsetcommunication is only used in different …
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I am a single cell RDS file with multiple samples and batches. Should I use the integrated RDS file or the merged file.
Because I found that when I use the following two treatments, the results may n…
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Hello !
I'm performing a multivelo analysis on a complex tissue with more than 10 well-represented cell types. When I perform the analysis on the whole sample, it work just fine.
However, I'm mainly…
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## Description
Trouble using vizgen data with sq.read.vizgen(). Function is expected 8 columns in metadata file mine has 9
## Minimal reproducible example
```python
adata = sq.read.vizgen(
…
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##------ Mon Jul 29 12:08:23 2024 ------## ******* 8th: scPagwas_perform_score function start! ********
* Get Pathways'rankPvalue for each celltypes!
[1] "Epithelial cells"
[1] "T cells"
[1] "Endo…