Simon Frerich
Simon Frerich
Do you have any recommendations about the concatenation of Visium spots from multiple samples into a single anndata object? Is it valid to analyse them together using the single-cell pipeline?...
It would be super useful if you could add an option to `tg.plot_genes_sc()` and `tg.plot_cell_annotation_sc()` so that the tissue image is shown in black and white. The pink colour of...
How does CellChat handle redundant signalling? In other words, what happens if multiple ligand sources and receptor targets from the same ligand-receptor pair are spread across cell groups? Can communication...
- [x] Additional function parameters / changed functionality / changed defaults? - [ ] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?...
Fixing bug in filter_missval(): keep$rowname is vector of character strings but should be row index, hence turned to integer. Error in .SummarizedExperiment.charbound(i, rownames(x), fmt): [i,] index out of bounds: 10...
Typo pip
Typo?
Hi, I am having the same issue as in #12 when trying to load adata$uns. ``` Error in eval(expr, envir, enclos): Conversion from numpy array type 20 is not supported...
Using [this](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/napari_rois.html#) tutorial for MERFISH data, I found that the output of polygon_query(sdata, my_napari_annotation) does not contain any filtered table, despite my_napari_annotation covering multiple cells. Is there something missing in...
Hi, I wonder if you can provide some guidance/tutorial how to best apply ClusterMap to MERFISH data. Would be highly appreciated. Best, Simon