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Since I can't use my seurat objects averaged cell type matrix directly (for deconvolution) since I keep getting the quadprog solve error
```
Error in quadprog::solve.QP(D/sc, d/sc, A, bzero) :
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Dear Rui,
your simulation method is really helpful for me. And I have a question about the annotation.
Did you find the simulated data from https://github.com/CaiGroup/seqFISH-PLUS ?
If so, in th…
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**Describe the bug**
The code needs to run smoothly on GPUs as well as on CPUs. For GPUs, there are inconsistency in loading the data to the device.
**To reproduce**
Just run the notebooks.
**…
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I encountered an error when running `insitutype() `for supervised cell typing on dataset of single slide.
```
load("~/hsdata/2021_Data/GeminiAnalysis/Scribe_team/SMI_tertiary/R4614_MN1K_wholeB/r…
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**Describe the bug**
ImportError: cannot import name 'FilterFunctionName' from 'gtda.mapper.filter'
**To reproduce**
I was in the 3rd cell of the code and an issue cames while running the impo…
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#### Background
The TAP and the commercial DA will both use Seurat objects rather than Giotto objects. But exactly the format of that Seurat object remains to be determined.
#### Takeaways:
- Fa…
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**Is your feature request related to a problem? Please describe.**
The pain is that, most often, plain datasets are not in the right input format or do not have the designed statistical caracteri…
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The proposal is to specify a **logical execution time** (**LET**) for a reaction as follows:
```
reactor Foo {
input in:int;
output out:int;
reaction(in) -> out after 10 msec {=
…
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Hello Everyone!
I'm Daniel, a PhD student at [saezlab](https://saezlab.org/). I'm opening this GitHub issue motivated by our recent comparison of cell-cell communication methods[1] as well as disc…