Malte Kuehl
Malte Kuehl
Resolves #245. The goal of this PR is to provide the necessary basis to facilitate contribution from different people to the python code in the future while at the same...
Currently the python scripts in the `./scripts/` folder do not seem to strictly follow any linting, formatting, typing or style guide, docstrings are often missing and no configuration files to...
Add support for sample-/gene-dependent normalization factors (e.g., length offsets from pytximport)
## Request I would like to propose support for sample-/gene-dependent normalization factors to enable the use length offset matrices from [pytximport](https://pytximport.readthedocs.io/en/latest/start.html), a full-featured Python implementation of tximport, similar to how...
#### What does your PR implement? Currently, `DeseqStats.lfc_shrink` does not respect `self.quiet` when printing `self.results_df` at the end of the method. This PR adds checks for `self.quiet` for the missing...
**PR Checklist** - [ ] Referenced issue is linked - [x] If you've fixed a bug or added code that should be tested, add tests! - [x] Documentation in `docs`...
Fixes #305 and closes #359. Adds support for normalization factors based on length provided by `pytximport`. Very much still a draft. Open issues: - Is the example dataset okay? Others...
Allows neighbor counts < k in `sc.pp.neighbors` by adding masking to `_ind_dist_slow`, enabling adaptive neighbor transformers. Draft for now, as I could not run tests locally or on CI (following...
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