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Hello,
Thank you for developing this nice tool.
I'm interested in analyzing allele-specific expression (ASE) in my single-cell RNA-sequencing (scRNA-seq) data. This data comes from offspring tissues…
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### Windows Terminal version
1.15.1862.0
### Windows build number
10.0.19044.1766
### Other Software
- Narrator
- NVDA latest version
### Steps to reproduce
- Run Narrator on NVD…
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Test runs are synthetic runs where the system is run dry - there is no actual cell present. Test cells are pretty easy to spot from looking at the XML. But possibly the pipeline will see the run befor…
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Hello!
When I was using scTE, I encountered some problems and I wonder if I can get some advice.
### Question 1: Preprocessing BAM Files with Filtered Barcodes from CellRanger Output
I'm ex…
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I was thinking it'd be cool if each cell of the notebook can be mapped onto a pn.pipeline.Pipeline().
For example:
Cell 1 / Page 1:
```python
import panel as pn
pn.extension()
pn.Tabs([0, …
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### Name of the tool
CellRanger ARC
### Tool homepage
https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
### Tool description
Add comp…
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Hi, thanks for the tool! I am currently comparing a few tools to establish a multi-omic single-cell RNAseq and single-cell ATACseq pipeline. I am trying HMMRATAC and saw in the paper that you created …
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This is a staging place for stuff to add to the Reconstrue Handbook, for how to use these tools.
- [Evaluation of UMAP as an alternative to t-SNE for single-cell data
(2018)](https://www.biorxiv.o…
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Dear author,
Thanks so much for developing the great tool. I recently applied it on a single nuclei data, and encountered some errors I have never met with 10x single cell data, here is the error:
…
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Hi
That's a great method! I'm wondering if, without the reference data and positive/negative markers (I only have the DAPI image and transcripts.csv), this method is still viable for cell segmentati…