feat: Implement DESeq2 in R instead of pyDESeq2

[yeising]

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✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch feat-DESeq2-from-pyDESeq2

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[cmeesters]

The test CI ist currently failing, because the input de_analysis/sorted_normalized_counts.csv for the rule generate_gene_query does not exist.

Honestly, the wildcards in deseq2 puzzled me. Also, will we need to invoke generate_gene_query several times or should we allow it to take multiple inpunts and merge them?

Perhaps, it is also a good idea to have a follow up PR to include a few extra code comments.