Gregor Sturm
Gregor Sturm
It would be nice if I could pass a custom callback function for parsing yaml files. There's already support for the native yaml loader and the OrderedDict yaml loader and...
When passing a boolean mask to `add_modality` (which is supported according to the type hints) using ```python mask = np.zeros((3000, 3000), dtype="uint8") mask [ 500:-500, 20:-500] = 1 ``` It...
Prettier requires a full-blown node installation and is rather slow. Alternatives would be welcome. > Maybe we soon don't need prettier anymore: https://biomejs.dev/ > > It doesn't have yaml support...
### Description of the bug I'm running the exact same flowcell, once with bcl2fastq and once with bclconvert. CheckQC only runs when bcl2fastq is selected as demultiplexer. I'd expect checkQC...
### Description of feature I suggest to add a process that checks Illumina Samplesheets for consistency before starting bclconvert/bcl2fastq. This ensures that errors are caught early with useful error messages...
### Description of feature In addition to the basic DE tutorial that shows the basic functionality of DE methods, we should have an advanced tutorial that shows how to build...
### Description of feature ### Description of feature They can be used to either perform tests on all cells, including the sample as random effect, or on pseudobulk when there...
### Description of feature Some of the methods are embarrassingly parallel, e.g. statsmodels, wilcoxon test. I suggest to use the following snippet from scirpy: * using joblib it is more...
### Description of feature When creating a complex contrast with `model.cond`, there should be a way to print out the actual contrast generated as a santity check for the user....
### Description of feature When inspecting a model object in jupyter, we should see a summary of the model, the input data etc. In jupyter, we could also show this...