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Hi Seurat team,
How can I extract the full counts matrix from a seurat object (with rows as features/genes and columns as cell barcodes). My seurat object is below.
```
str(seurat.obj_combined_…
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I downloaded the Lieber 10x single cell data in order to determine what
cell types express my genes of interest (I have a list of ~200 genes).
I am new to single cell data and singlecellexperiment …
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Hello,
I am very interested in your publication, but didn't see adipocytes population in your Fig. 1, only FAPs. I am interested to get the proportions of adipocytes and myocytes in skeletal muscle…
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Hi Alex,
I'm trying to analyze a snRNASeq experiment, but am running into trouble.
I've been following cellgeni's tutorial (https://github.com/cellgeni/STARsolo) for STARsolo, but have used you…
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## Information
### Proposed change:
Add `TST` as option for required attribute `Single Nucleus Buffer`
Current valid values are : NIB, 10x, Omni
---
### Dicussion link:
Email from Allison Fr…
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Hi Jeffrey and Ryan,
Thank you so much for developing this wonderful tool and we are actively using it for 10X scATAC-seq and multiome analysis. I'm following https://greenleaflab.github.io/ArchR_2…
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Full reindex on DEV to test out the round 5 efficiency updates from Karl's changes, but encounter hundreds of such errors:
```
[2024-06-22 07:00:07] ERROR in es_writer:95: Failed to write doc of u…
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Hi,
Thanks for the RCTD pipeline. I have been trying to run RCTD using my own reference snRNAseq data and 10x Visium.
I have been having trouble generating the input files. Getting various error m…
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Hi!
Thank you for developing a great tool! NicheNet matches what I want to clarify in my project.
So, I have been using NicheNet with my snRNAseq data from mouse brain. Since the prior model has b…
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I think the keepMax variable should correspond to the **minimum** between the number of non-empty droplets * 2 and the total number of droplets in the object. As it is now (max instead of min), it sel…