Forum: Will anyone want to use a PyDESeq2-based platform? How to improve my platform
I am developing an open-source platform that uses PyDESeq2 to perform differential expression analysis from raw count matrices and generate volcano plots.
Beyond volcano plot visualization, what species-agnostic downstream analysis features would be most valuable to include for deeper biological interpretation, assuming only raw counts and minimal or optional gene annotations are available?
https://github.com/chuang-DH/deg-volcano-platform https://deg-volcano-platform-6htpr5ugnf8ygqcwarfbe2.streamlit.app/
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Istvan Albert
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Chuang, D-H •
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Chuang, D-H •
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A volcano plot has almost no biological meaning - it is more of a QC plot that informs on the distribution of p-values and fold changes, in the end it is only useful it the data looks bad, in which case there results are suspect as well.
Overall your approach feels a bit backwards, a solution is looking for problems. You should approach it from the other perspective - have a problem, solve it, then look at generalizing it.