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Hello SPROD author!
Tools like Tangram or gimVI can utilize scRNA-seq data to predict and impute spatial data, but they seem to be unable to denoise contaminated data. Therefore, I am considering u…
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Hi,
I got an error probably related to get_cellfracs_seuratv3
> Error in split.default(x = cells.vector, f = ceiling(x = seq_along(along.with = cells.vector)/ncells)) :
It even occurs when…
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The dataset types in the gEAR portal are nice and tidy:
```
mysql> select dtype, count(dtype) from dataset group by dtype;
+-----------------------+--------------+
| dtype | coun…
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Hi Team,
I'm analyzing scrna seq data from different mice tissues. I'm following the standard pipeline - preprocessing, normalizing, feature selection, clustering - currently annotating cell types(…
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Hi, I have some unpaired scRNA-seq and scATAC-seq data, they are sequencing the same samples, but in separate scRNA-seq and scATAC-seq assays, so the cell barcodes are different in these datasets. How…
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Thank you very much for building this wonderful app for analyzing scRNA-seq data. However, recently i cannot connect to the website as well as app via shiny. Could you please solve this problem? Thank…
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Hi everyone,
I’m currently working on Xenium (10x Genomics) data analysis, which contains 321 targeted genes. To explore more, I would like to merge and integrate public data with my Xenium dataset…
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### Task motivation
Gene Regulatory Network (GRN) inference is pivotal in systems biology, offering profound insights into the complex mechanisms that govern gene expression and cellular behavior. Th…
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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…
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Hello,
I would be interested in trying your tool on some scRNA-Seq data with multiple donors and perturbations.
In the past I've used edgeR with a linear model à la (~ Donor + Treatment).
Sinc…