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Hello, when running 'imt_gsea', I encountered an error: 'TypeError: gsea() got an unexpected keyword argument 'perm_index'.' I've tried various methods but still can't resolve it. Can you help me? The…
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Hello,
I'm struggling with the type of data that you require for transcriptomics functions: what is the structure of the dict `gene_exp` that you need?
```
def eFlux(model, gene_exp, scale_rxn=…
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Hi everyone! I am a PhD candidate and a very beginner of spatial transcriptomics. Please help me...
I have CosMx dataset of 3 different samples (S0, S1, and S2) and try to analyze and compare them …
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Hey
I'm trying to open a Visium HD data (with 600k spots/bins) but it simply kills the terminal whenever I open it:
```
>>> adata = po.CreatePiannoObject(
... data_path=data_path, count_…
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Dear alegiac95,
![123](https://github.com/alegiac95/Imaging-transcriptomics/assets/111960642/70c80529-f188-4d5d-918e-060f447b8838)
Thank you for your toolbox "Imaging-transcriptomics".
I have …
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Hello everyone,
I am trying to follow this tutorial page:
https://stlearn.readthedocs.io/en/latest/tutorials/Integration_multiple_datasets.html
But when I plot the adata_concat, it returns t…
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Can DIPAN be used in long-read transcriptomics such as nanopore reads?
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Integrate data and workflows from the [Galaxy reference based transcriptomics training](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html) w…
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We need enzyme data for the BMCA workflow. `EFlux2` implements rules to deal with multiple genes dictating a reaction.
Take the upper bounds assigned by `EFlux2` and create a dataset using these up…
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Hi,
Wonderful job!
I have searched through many articles and am looking for a Shiny app that can handle spatial transcriptomics data in a similar manner to how [Shinycell](https://github.com/SGDDN…