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Hi,
I got this error when calling `dds.deseq2` on my data:
```
---------------------------------------------------------------------------
IndexError Traceback (…
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Hey, sorry incase my questions are naive
1)I am trying to use PyDESeq2 using continuous covariate (age) taking into account, sex,cmv serotype etc.
in order to get differentially expressed genes th…
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Hi @noriakis,
I'm making pathway diagrams for the Lysine Biosynthesis pathway using ggkegg, but for some reason the mapping between reaction numbers and ec numbers doesn't work for some nodes. For …
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I am trying to study how different cancer types and sex affects the cell abundances in different cell types.
`design_matrix
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Issue Description:
The pydeseq2.dds.DeseqDataSet class in the 0.4.4 release of the PyDESeq2 package does not recognize the keywords 'n_cpus' and 'n_processes', despite both of them being documented…
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Hi @noriakis,
Is it possible to use this package to visualize LFCs for target genes on raw KEGG Maps? For example, this image:
![image](https://github.com/noriakis/ggkegg/assets/148665071/8826c8bd…
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Hi @noriakis,
Is there any way to improve the resolution of a graph made using the overlay_raw_map function? I made a pathway diagram using some of your code from the documentation, but the resolut…
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Hi @noriakis,
I'm currently trying to visualize the "pentose phosphate" pathway in kegg using the ggkegg package, but when I create a diagram many of the nodes are not connected to each other, and …
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Hey,
currently you're creating pseudobulks by summing up counts (perfectly fine) but we need pseudobulks that take the median for an implementation of DIALOGUE. We're currently using a custom imple…
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Dear authors,
First of all, the miloR package looks incredibly useful and generally well-documented.
My issue is about the lack of documentation for the output table of `testNhoods()`. The docu…