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# 2024 phenotype data
## 2024 phenotype data
Scatter plot of Alkaloids vs Delta CT (both normalized and OG data).
![RplotAlkaloid_vs_DeltaCTadj_2024](https://github.com/DarrianTalamantes/Mappin…
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If one runs the Jacobian calculation with sub-sampling enabled such as follows: `dyn.vf.jacobian(adata, regulators=top_pca_genes, effectors=top_pca_genes, sampling="velocity", sample_ncells=2000)`, su…
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### Description of feature
The `--relevel `parameter in rnadeseq is primarily there for modeling in DE analysis ( i assume/recall). I just noticed that it has no influence on the ordering of the samp…
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Some code for filtering, analysis, and plotting is duplicated between `src/PCA.py` and `src/plot_PCA.py`.
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Firstly, thank you for putting together such a useful tool!
Apologies in advance if this is a naive issue as I am relatively new to R and scRNAseq analysis. I am trying to use Lamian to compare pse…
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We have a rich set of examples covering a very broad range of issues, but they're not necessarily easily discoverable via the section on the bottom of the API pages.
This meta-issue is to keep trac…
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Want to use monocle2 to show the trajectory. But in the **plot_pc_variance_explained** , it showed the warning, and I can not make sure how many pc are explained. So I set the parameter **num_dim = 10…
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Hello, I am trying to plot my cluster assignment and saw this example code on your documentation:
```
ggplot2::ggplot(res$complete_data,ggplot2::aes(x,y,color=factor(res$clusters))) +
ggplot2::g…
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Dear Sir,
I am running GAPIT with multiple analysis function, run is stuck on "Calling prcomp..." step.
My gapit function:
for(i in 2:ncol(myY))
{
myGAPIT
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### Discussed in https://github.com/satijalab/seurat/discussions/9442
Originally posted by **bbmorris1** October 31, 2024
I have scRNAseq from a tumor cell line +/- drug treatment (sample 1 = …