Refactor repository
This merge request should bring the repository into a organised state, as required for milestone v2.0.0.
Regarding the structure, we discussed following outline, which should be adapted until merging:
-
subdirectories Tools
- (like in the notebooks) tools.embedding ....
- tools.preprocessing
-
subdirectories for utilities
- utils.adata
- utils.io
- utils.bioutils
- utils.analysis (basic)
-
directory for plotting related code:
- general plotting functions
- embedding
- qc plotting
- interactive plots (see where)
- marker gene plots
- nucleosome_signal
- receptor_ligand