Develop a codebase to address the the following regarding calcification gene activity in corals:

Porites (peve) exhibits constitutive higher gene body methylation (GBM) in key calcification genes (e.g., Ca-ATPase, Carbonic Anhydrase) than Acropora (apul)  and Pocillopora (ptua) compared to other genes

Data neccessary to test the hypotheses 

Expression matrices of calicification genes across timepoints and treatments for each species.

https://raw.githubusercontent.com/urol-e5/timeseries-molecular-calcification/refs/heads/main/M-multi-species/output/33-biomin-pathway-counts/apul_biomin_counts.csv

https://raw.githubusercontent.com/urol-e5/timeseries-molecular-calcification/refs/heads/main/M-multi-species/output/33-biomin-pathway-counts/peve_biomin_counts.csv

https://raw.githubusercontent.com/urol-e5/timeseries-molecular-calcification/refs/heads/main/M-multi-species/output/33-biomin-pathway-counts/ptua_biomin_counts.csv


Annotation file
M-multi-species/output/12-ortho-annot/ortholog_groups_annotated.csv



Gene Body Methylation 

Acropora pulchra
https://raw.githubusercontent.com/urol-e5/timeseries-molecular-calcification/refs/heads/main/D-Apul/output/40-Apul-Gene-Methylation/Apul-gene-methylation_75pct.tsv 

Porites evermanni
https://raw.githubusercontent.com/urol-e5/timeseries-molecular-calcification/refs/heads/main/E-Peve/output/15-Peve-Gene-Methylation/Peve-gene-methylation_75pct.tsv 

Pocillopora tuahiniensis
https://raw.githubusercontent.com/urol-e5/timeseries-molecular-calcification/refs/heads/main/F-Ptua/output/09-Ptua-Gene-Methylation/Ptua-gene-methylation_75pct.tsv