Update rpy2 to pydeseq#19

Merged

mehdijoodaki merged 9 commits intoCostaLab:mainfrom

CharlieNotChaplin:update_rpy2_to_pydeseq

Apr 7, 2026

Commits on Mar 23, 2026

Updated function compute_diff_expression from limma (R) to pydeseq2 (python). Added saving of under- and overregulated genes. Removed now obsolete helper functions.
CharlieNotChaplin
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Fixed description for updated diff exp method.
CharlieNotChaplin
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Commits on Mar 24, 2026

Commits on Mar 31, 2026

Updated functions to replace rpy2 with pydeseq. Fixed imports and docstrings. Unified double functions: volcano_plot and gene_annotation_cell_type_subgroup. Copied finished and tested function file…
CharlieNotChaplin
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Removed all old unused functions (mainly rpy2 based functions)
CharlieNotChaplin
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Commits on Apr 1, 2026

Relaxed version constraints in setup.py, updated README and cell_gene_selection.py function calls accordingly.
CharlieNotChaplin
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Commits on Apr 7, 2026

Updated tutorial with the correct download link for the PDAC dataset.
CharlieNotChaplin
committed