LLehner
LLehner
**IMPORTANT: Please search among the [Pull requests](../pulls) before creating one.** ## Description - Added function to build design matrix containing distances to anchor points which can be used for plotting...
## Description Adds a method in ```tools``` to calculate embeddings of variables by their counts aggregated by distance. ## Example usage `import squidpy as sq` load example data set `adata...
Add reader for Stereo-seq files. TODO: - [x] Read cellbin.gef completely - [x] Fix LabelsModel - [x] Fix ShapesModel - [x] `counts_per_cell` present in .obs? - [x] Update `table.obsm["cellBorder"]` -...
Add reader for seqFISH data.
## Description Adds a function that calculates niches using different strategies. The initial function calculates niches based on neighborhood profiles similar to [here](https://github.com/immunitastx/monkeybread/blob/main/src/monkeybread/calc/_neighborhood_profile.py). This PR will get updated with methods...
Hello, thank you for this great tool. Currently we are trying to redo the [HFSP curve](https://academic.oup.com/bioinformatics/article/34/13/i304/5045799) using foldseek instead of mmseqs2. When using identical data we noticed a shift downwards...
The `ImageTilesDataset` class cannot be used if the table you want to work with is not called "table", since there are lines where this name is hard-coded, even though the...
A first draft tutorial for calculating niches with squidpy. To be updated, as updates are made to https://github.com/scverse/squidpy/pull/831.
An updated Xenium tutorial for analysis using Squidpy, but instead of only working with `anndata`, `spatialdata` is used. @LucaMarconato please let me know if things should be added. So far...