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**Describe the bug**
Hello. I seem to be getting an error at the get_search_space step in the scenicplus pipeline with snakemake. Any immediate thoughts about why this could be? Should my region se…
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Hi, thank you very much for developing such a helpful tool! I am interested in mapping multimodal data such as SHARE-seq to reveal spatial patterns of chromatin accessibility, but I don't know how to …
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Hello,
I have a question about measuring the concordance between bulk and sc DE tables. In your script, you used 6 different methods to generate DE tables when the input is bulk RNA-seq data. Whic…
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# Data overlap
## Generate a `data overlap matrix`. Overlapping to the `ATAC-Seq differential accessible regions`
- [x] **ChIP-Seq:** `TRUE` or `FALSE` of there is an overlap between ATAC-Seq an…
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Hello,
I am experiencing an issue with the `Scissor` function in Seurat while analyzing single-cell RNA-seq data. I am trying to integrate my Seurat object with Scissor for further analysis, but I …
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Create an endpoint to generate the csv needed by the data sankey diagram. Diagram [here](https://software.docs.hubmapconsortium.org/data-sankey/index.html) example csv [here](https://github.com/hubm…
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Current proposal:
There are only two levels of topics, the main card, and tags within the card
```
- Help (one for each project e.g., Scanpy, Muon, ...)
- Tags = project subpackage or releva…
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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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**Describe the bug**
when I test the muon pipeline by using data of 6400cells, error happens when run 'mu.pp.neighbors(mdata, key_added='wnn')'' like : *** Error in `python': malloc(): smallbin doub…
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Hi @dg520 ,
Hope you are doing well :)
I have been trying to use IRFinder on BAM files generated by cellranger to quantify IR. On doing so, I get the following error :
```
WARN: This sampl…