Ara_data.hdf5
===================================================================================================
Contains:
	counts: (matrix)	22271 x 16641 
		- Merged arabidopsis scRNA seq expression data from 4 sources

	coldata: (dataframe)	16641 x 6
		- Cell meta data

	rowdata: (dataframe)	22271 x 1
		- Gene meta data

	embedding: (dataframe)	16641 x 3
		- UMAP embedding


TM_data.hdf5
===================================================================================================
Contains:
	counts: (matrix) 	23433 x 44949
		- Merged Tabula Muris Smart-seq expression data
	
	coldata: (dataframe) 44949 x 8
		- Cell meta data

	rowData: (dataframe) 23433 x 2
		- Gene meta data
	
	embedding: (dataframe) 44949 x 3
		- tSNE embedding


20200625_tagr_nodups.Rdata
===================================================================================================
Contains:
	oa.mat: (dataframe) 	271,068 x 18
		- Table of 1-to-1 orthologs between a pair of species (Gene symbol and Ensembl IDs),
		the number of algorithms predicting the orthologs, and their coexpression conservation +
		specificity scores


spe37_divergence_timetree.csv
===================================================================================================
Contains:
	counts: (matrix) 	37 x 37
		- Upper triangular matrix of estimated species divergence times for all pairs of 37 species
		from timetree.org


scripts/
===================================================================================================
Contains:
	ortholog_scores_1to1_topN.R: (script)
		- Functions to calculate coexpression conservation and specificity scores using only 1-to-1
		orthologs given a species pair (species1, species2)
		
	ortholog_scores_manytomany_topN.R: (script)
		- Functions to calculate coexpression conservation and specificity scores using many-to-many
		orthologs given a species pair (species1, species2)
			

geneInfo/
===================================================================================================
Contains:
	<species>_info.csv: (dataframe) 	
		- Table of genes present in the species' coexpression network and corresponding IDs in
		other databases (ex: Entrez, Ensembl, OrthoDB, etc.)


orthoNets1-1/
===================================================================================================
Contains:
	<species2 Taxonomy ID>-<species1 Taxonomy ID>orthologMatrix.Rdata:  	
		- net11: dataframe with list of 1-to-1 orthologs shared by the species pair


orthoNetsN-M/
===================================================================================================
Contains:
	<species2 Taxonomy ID>_<species1 Taxonomy ID>_NM_orthologmat.Rdata:  	
		- om: matrix mapping many-to-many orthologs across species pair. Rows and columns contain
		OrthoDB IDs of genes in species2 and species1, respectively. Matrix entries 1 indicate
		genes are many-to-many orthologs (either 1-to-1, or part of gene family), and 0 otherwise.
		

coexp_cons/
===================================================================================================
Contains:
	<species1>_<species2>_CoCoBLAST_scores.hdf5:  	
		- sp1_netid:
			List of genes from coexpression network of species1 (Gene symbol or Ensembl IDs)
		
		- sp1_orthoid:
			OrthoDB IDs corresponding to genes in sp1_netid
			
		- sp2_netid:
			List of genes from coexpression network of species2 (Gene symbol or Ensembl IDs)
		
		- sp2_orthoid:
			OrthoDB IDs corresponding to genes in sp2_netid
			
		- ortho_map:
			Dataframe of many-to-many orthologs in species pair
			
		- fc_scores: <sp1_netid> x <sp2_netid>
			Matrix of coexpression conservation scores for all gene pairs across species.
			Scores for many-to-many orthologs can be shortlisted when combined with ortho_map.
			
		- sc_scores: <sp1_netid> x <sp2_netid>
			Matrix of coexpression conservation specificity scores for all gene pairs across species.
			Scores for many-to-many orthologs can be shortlisted when combined with ortho_map.
			
		- chunkSize:
			Chunk size used to store the dataset