Week 7

• PyDESeq2 documentation: https://pydeseq2.readthedocs.io/en/stable/

• PYDeSeq2 paper: https://pmc.ncbi.nlm.nih.gov/articles/PMC10502239/

• Roary Pangenome analysis (gene annotations and presence/absence data): https://sanger-pathogens.github.io/Roary/

• NCBI Run Tables (metadata): Some Field Descriptions/Documentation

• hypothesis_testing notebook from Tuesday

• “raw” data https://drive.google.com/file/d/1IsrR-MFhrEWUFD45N5o_RcXVeQCYYyHV/view?usp=sharing