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:

1. subdirectories Tools

   • (like in the notebooks) tools.embedding ....
   • tools.preprocessing

2. subdirectories for utilities

   • utils.adata
   • utils.io
   • utils.bioutils
   • utils.analysis (basic)

3. directory for plotting related code:

   • general plotting functions
   • embedding
   • qc plotting
   • interactive plots (see where)
   • marker gene plots
   • nucleosome_signal
   • receptor_ligand