Malte Kuehl

Provide (more) consistent linting and formatting with black and flake8

2

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...

Consistent python style, linting and formatting for `scripts` folder

3

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...

## 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...