tidybulk

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stemangiola

Play the same strategy we have applied for the immune map paper to resolve two confounding factors that are not of interest. `simplify_design_matrix(suffix = "__simplified")` This function will take a...

stemangiola

Improve the documentation for `tidybulk`

29

- improving examples for methods - solving documentation warnings (when packages are loading or installing) - Improving methods' argument description - improving the transparency of the method used in the...

stemangiola

I am opening this issue as a notification because `tidybulk` is listed [here](https://cran.r-project.org/web/packages/Seurat/index.html) as a package that relies (depends/imports/suggests) on Seurat. As you may know, we recently released Seurat v5...

Gesmira

When using quosures to define the .abundance_scaled column name in the internals, the environment gets carried along and a 1 Mb SummarizedExperiment becomes a 400Mb RDS file. it can be...

stemangiola

Hello @mblue9, I have a mystery, and I was wondering if you're careful and fresh, I can spot where the arrow is. https://github.com/stemangiola/tidybulk/actions/runs/5369140637/jobs/9740360362?pr=272#step:20:564 I have this WARNING just for the...

stemangiola

The first element of assays in SE might be a matrix when using DESeq2 method

6

The related issue ``` > library(tidybulk) ======================================== tidybulk version 1.12.0 If you use TIDYBULK in published research, please cite: Mangiola et al. tidybulk: an R tidy framework for modular transcriptomic...

xiangpin

pathway analysis using tidybulk

8

Could you please point me to github repos or links where you have successfully tested pathway analysis (GSEA and Overrepresenation analysis) tidybulk functions for pathway analysis? Some of the workshop...

adityamahadevaniyer

stemangiola