Gregor Sturm

autoreload feature

11

While developing interactively, it would be fantastic if the modules are re-loaded automatically in the background every time a module has changed. This is how the [`%autoreload`](https://ipython.org/ipython-doc/3/config/extensions/autoreload.html) magic works in...

process.ext set with withName overrides configuration of all processes

7

## Bug report ### Expected behavior and actual behavior * Expected: Options set with `withName` only affect the corresponding process(es) * Actual: If process.ext gets initalized for all processes, updating...

Loading dropdown component with many items is slow

16

Similar to the issue described in #103, I am having trouble with the speed of very long dropdown lists (40k+ items). However, in my case it's not the speed of...

Design matrix is not full rank (on example that works in edgeR)

2

[Soneson et al, 2018, NMeth](https://www.nature.com/articles/nmeth.4612#references) recommend to add the fraction of detected genes as a covariate to the linear model for DE testing: ``` ~ group + n_genes ``` (instead...

ZINB noise model

2

[Van den Berge et al, Genome Biol 2019](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1406-4) argue that using a Zero-inflated negative binomial (ZINB) model significantly boosts the performance of differential gene expression analysis on single-cell data. Using...

Results changed from v0.6.13 to 0.7.1

2

Hi, while experimenting with diffxpy, I noticed that the results changed since I upgraded from v0.6.13 to v0.7.1. Is that intentional? ### The setup: I added diffxpy to the DE...

Update full and reduced scale parameters in documentation to be consistent with code: https://github.com/theislab/diffxpy/blob/dfe8304db9bba93dfc7efebebecdc62512ca6c16/diffxpy/testing/tests.py#L862-L865 While being mathematically equivalent (I think...) I got confused when trying to understand the code.

Lambda indexer for anndata

6

With pandas data frames a pattern I use very commonly is ```python df_with_very_long_descriptive_name.loc[lambda x: x["fruit"] == "banana", :] ``` I was wondering if it would be possible to have lambda-based...

scverse datastructure for AIRR data

41

Now that scirpy is part of scverse, we could think of an improved data structure for scAIRR data. See also the discussion at https://github.com/theislab/scanpy/issues/1387. The challenge with scAIRR data is...

Implementing the changes suggested in #327. Close #327 Close #184 Requires * pre-release version of awkward array * Anndata installed from the `val_shape` branch --- **TODO** - [ ] store...