Michael Strasser

Hi, I ran into this weird bug: pynndescent works fine when using a smaller number of n_jobs (anything up to `n_jobs=17` works) , but above, it just throws a segmentation...

Hi, as far as I understand weightnorm-initialization, you calculate the mean/std of the 'preactivations' (without the nonlinearity applied) and use these to initialize the weights/biases. In `weightnorm.data_based_init()`, it is implicitly...

Changing dotsize (radius) of cells in an already built cellbrowser

5

Hi all, I'm wondering if there's a quick way to change the dotsize ("radius" in cellbrowser.conf) of cells in an already existing cellbrowser (built into a html site via `cbBuild`)....

Hi, I just noticed that the default values of `Graph.dump_nodes()` mentioned in the docs are different than what the code acutally does. From the python docs: ``` > G.dump_nodes? ......

git-fat pull and git-fat init

5

Hi, while using git-fat, I came across a small "issue": If one doesn't execute "git fat init" after cloning a repo that uses git-fat, the pull just wont succeed (it...

Update _tileplot.py for plotnine >=0.13

1

With `plotnine>=0.13` they changed the interface of `facet_grid` (see [Release notes](https://github.com/has2k1/plotnine/releases/tag/v0.13.0)); there's not more argument `facets` and doing something like [the tutorial](https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html) ```python li.pl.tileplot(liana_res=lr_res, fill = 'expr', label='padj', label_fun =...

[BUG] local variable 'beta_init' referenced before assignment

2

**Describe the bug** Under certain circumstances, `dds.deseq2()` crashes with a `UnboundLocalError: local variable 'beta_init' referenced before assignment` (originating in [pyydeseq2/utils.py](https://github.com/owkin/PyDESeq2/blob/7a4032d6cd0948184a477a2b21cc982501552147/pydeseq2/utils.py#L562)) From what I can tell, two conditions have to be...

Hi, I often need to look up what window `i` in CNV space (`adata.obsm['X_cnv'][:,i]`) corresponds to in gene space (i.e. which chromosome, which genes, which coordinates). Might relate to #50...

Hi, I just ran into this somewhat obscure bug: If you use **integers** to label your sets, under certain circumstances, `UpSet.plot()` returns *wrong* intersection sizes. I tracked the issue down...

Hi, just ran into a bug when using the `--sequential` flag in the build script. Essentially, it overwrites the CLI-args with something else (the content of `settings["targets"].items()` and fails later...