Script to do PCA and DEseq2 analysis
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This script performs PCA and DEseq2 analysis, output differentially expressed genes, and generate MA plots and PCA plots. 

Related to Figure 5B, as well as Figure 5-figure supplements
 

Directory Structure:
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Input   |
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1. The Count supermatrix .csv file generated using the '2_getCombinedCountMatrix_220805_codechk.pl' script
2. Experimental design .csv file that contains library name, sex, feeding, batch, and condition (a complex variable with all the info). 

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Plots   |
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This is where the PCA plots and MA plots will be stored.


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Output          |
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This is where all the DEseq2 comparisons and normalized counts will be stored.