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Added automatic gene labeling & reformatting of notebooks

Mette Bentsen requested to merge notebook_structure into dev

A few changes:

  • Added automatic gene labeling based on species given
  • Update of tests for utilities and marker genes modules
  • Changes to the notebooks to make it more clear where to input data
  • Started formatting notebook 3 to get ready for PCA/batch correction options

I branched this from one of the other pull requests, so I think we should just merge those before this one :-)

Edited by Mette Bentsen

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