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Batch Correction DESeq2 #447

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PaulJonasJost opened this issue Jan 31, 2025 · 0 comments
Open

Batch Correction DESeq2 #447

PaulJonasJost opened this issue Jan 31, 2025 · 0 comments
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@PaulJonasJost
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enhancement New feature or request fixed but not released Solved the issue but still in develop branch.

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While Batch Correction in DESeq is handled correctly, we want to also be able to visualize batch-corrected data in e.g. PCA. For this, vet-transformed data needs to b run thrugh batch correction additionally.
@PaulJonasJost PaulJonasJost added the enhancement New feature or request label Jan 31, 2025
@PaulJonasJost PaulJonasJost self-assigned this Jan 31, 2025
PaulJonasJost added a commit that referenced this issue Jan 31, 2025
@PaulJonasJost
Moved all relevant functionality outside of base server. Will be used…
7546b33 
… for code creation Later!

Addtionally closes #447, Closes #435
And fixes a Small bug in the report where the batch formula and regular formula of deseq processing would be swapped
PaulJonasJost added a commit that referenced this issue Feb 3, 2025
@PaulJonasJost @LeaSeep
R code revamp for data selection and preprocessing (#448)
8b1ce6c 
* removed unused file

* first step: made data selection a function to outsource actualy processing. Done for future bulletproofing of R Code Snippets

* Tmp commit

* Moved all relevant functionality outside of base server. Will be used for code creation Later!

Addtionally closes #447, Closes #435
And fixes a Small bug in the report where the batch formula and regular formula of deseq processing would be swapped

* removed browser

* unnecessary komma

* We should remove this rather old info

* Update program/shinyApp/R/util.R

Co-authored-by: Lea Seep <[email protected]>

* non global assignment

---------

Co-authored-by: Lea@Mac <[email protected]>
Co-authored-by: Lea Seep <[email protected]>
@PaulJonasJost PaulJonasJost added the fixed but not released Solved the issue but still in develop branch. label Feb 6, 2025
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