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…python). Added saving of under- and overregulated genes. Removed now obsolete helper functions.
…strings. Unified double functions: volcano_plot and gene_annotation_cell_type_subgroup. Copied finished and tested function files from branch update-function.
…_selection.py function calls accordingly.
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Update the following functions from library rpy2 ro pydeseq2:
compute_diff_expressionwith new helper functionscheck_rawandfilter_genesvolcano_plot,gene_annotation_cell_type_subgroupvolcano_plot_ps(merged withvolcano_plot, now in ploting.py),get_pseudobulk_DE,compute_pseudobulk_DE,compute_pseudobulk_PCA,gene_annotation_cell_type_subgroup(merged with function with the same name in ploting.py to avoid conflict, now in ploting.py)rpy2, added package requirementpydeseq2>=0.5.1,<0.5.3Additionally: Added docstrings for all functions, removed conflicting paths and variable names