DEG/DAR Notebook
We currently provide the 05_marker_gene notebook for the RNA analysis which also includes a DEG (Differentially expressed genes) section, but we are missing a similar notebook for the ATAC analysis.
The first question would be if we even need two separate notebooks or if we can combine the notebooks into one general notebook.
The marker gene identification in the ATAC analysis is most likely going to look identical to the one in the RNA analysis.
How well does the DEG(RNA) compare to the DAR(Differentially accessible regions)(ATAC)?
If it is easily possible to combine the DEG/DAR functionality into one wrapper function we should combine the analysis into one general notebook.
If the notebooks are going to be separate we at least need to clean up the 05_marker_gene notebook. The notebook currently contains too many lines of code. This should be hidden behind some wrapper function(s).
The RNA notebook also uses DEseq2 as an additional option for the DE analysis, currently running with R, which is causing some problems as described here (#75 (closed)).
As described in the issue we should switch to the python implementation of DESeq2.
We agreed on a consistent format regarding current and new notebooks. The rules regarding those formats can be found here: #239