Gregor Sturm
Gregor Sturm
### Description of feature Currently, models and contrasts to compare are defined in the `contrast.csv` file as follows: ```csv id,variable,reference,target,blocking ``` This limits contrasts to pairwise comparisons of a single...
### Description of feature As discussed in https://github.com/nf-core/differentialabundance/pull/420 some methods have a stochastic component and are not deterministic unless setting a random seed. While @pinin4fjords argues that he doesn't want...
### Description of feature Functional analyses are often more easier to interpret than the raw list of differential gene expression analyses. Let's use this issue to get an overview of...
### Description of feature SummarizedExperiment objects are widely used Bioconductor data structure that keeps track of column, row annotations and multiple data matrices. Using SummarizedExperiments avoids some common pitfalls such...
### Description of feature In #362 we suggested to support more complex models and contrasts. This issue is to explore and find a consens on how to define contrasts for...
### Description of feature It's neat that there's the ShinyNGS app to interactively explore the pipeline results. However, it's a bit cumbersome to fire up a shiny server to run...
I have a spatialdata object with 49 Visium samples. It looks like this: sdata ``` SpatialData object, with associated Zarr store: /cfs//02_nfcore_spatialvi/output/aggregation/data/merged_sdata.zarr ├── Images │ ├── 'study1_sample1_hires_image': DataArray[cyx] (3, 2000,...
When attempting to `render_shapes` with a color key or a table key that does not exist, spatialdata-plot just plots everything grey. I would expect it to raise a KeyError instead....
`scanpy.pl.spatial` has a argument `bw=True` that allows to plot a background image in grayscale. I find that useful when plotting shapes on top of an image because the pink H&E...
### Description of feature After factoring out the differential expression visualizations into [deres](https://github.com/scverse/deres), I've been thinking if it would also make sense to make a separate package for the differential...