Gregor Sturm
Gregor Sturm
### 1. use decoupler I think a few sections of the DE section could be cleaned up by using decoupler functions instead of custom ones: * decoupler already has a...
**Is your feature request related to a problem? Please describe.** Most linear models support passing designs as design matrices and contrasts as contrast vectors. This is the "smallest common denominator"...
It would be great to have a `gene_symbols` argument to render_shapes and render_points, similar to what scanpy has in all (most?) plotting functions. The goal is being able to use...
I'd suggest you make all the plotting parameters keyword-only arguments, e.g.: ```diff def render_shapes( self, elements: list[str] | str | None = None, color: list[str | None] | str |...
Hi all, I was wondering about the API design of spatialdata-plot: Why did you decide for requiring a `pl` before every plotting command in a "plotting pipeline", e.g. ```python sdata.pl.render_images().pl.render_shapes(color="KRAS").pl.show("downscaled_hires")...
Closes #18
I feel `rpy2` is unreliable, the R packages are cumbersome to install and a lot of additional dependencies. On top of that, the R methods are relatively slow compared to...
inferCNV uses a [hidden markov model](https://github.com/broadinstitute/inferCNV/wiki/inferCNV-HMM-based-CNV-Prediction-Methods) to turn the smoothed gene expression into genomic regions that are subject to CNV. Would be nice to implement a similar feature here.
### What kind of feature would you like to request? Additional function parameters / changed functionality / changed defaults? ### Please describe your wishes It would be nice if `sc.get.aggregate`...
I am having issues installing a library from a tarball. Installing the same library from the source folder works without issues. Installing the same tarball with `R CMD INSTALL` also...