Read in gene count matrices from the three species. Note they are from 4 timepoints
(TP1, TP2 etc). Using the corresponding lncRNA expression matrices and CpG methylation
data, determine how DNA methylation and lncRNA potentially regulate expresssion
either in concert or separately. If any genes are found to be regulated, also determine
if any of these are Biomineralization genes based on the Biomineralization gene matrices provided (these are simply 
a subset of the full count matrices.)


Gene expression count matrices 

Acropora pulchra
https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-RNAseq-alignment-HiSat2/apul-gene_count_matrix.csv 
 
Porites evermanni
https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/02.20-E-Peve-RNAseq-alignment-HiSat2/peve-gene_count_matrix.csv 

Pocillopora tuahiniensis
https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/02.20-F-Ptua-RNAseq-alignment-HiSat2/ptua-gene_count_matrix.csv 
 
long non-coding RNA

Acropora pulchra
https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries_molecular/D-Apul/output/31.5-Apul-lncRNA-discovery/lncRNA_counts.clean.filtered.txt

Porites evermanni
https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries_molecular/E-Peve/output/12-Peve-lncRNA-discovery/lncRNA_counts.clean.filtered.txt

Pocillopora tuahiniensis
https://raw.githubusercontent.com/urol-e5/timeseries_molecular/refs/heads/main/F-Ptua/output/06-Ptua-lncRNA-discovery/lncRNA_counts.clean.filtered.txt 


CpG Methylation 

Acropora pulchra
https://gannet.fish.washington.edu/metacarcinus/E5/20250903_meth_Apul/merged-WGBS-CpG-counts_filtered_n20.csv 


Porites evermanni
https://gannet.fish.washington.edu/metacarcinus/E5/Pevermanni/20250821_meth_Peve/merged-WGBS-CpG-counts_filtered_n20.csv 

Pocillopora tuahiniensis
 https://gannet.fish.washington.edu/metacarcinus/E5/Ptuahiniensis/20250821_meth_Ptua/merged-WGBS-CpG-counts_filtered_n20.csv 


Biomineralization gene matrices

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