Intermediate results using the IMR90 and GM12878 cell lines for detection of spatial dependency in quantitative gene expression in the 3D genome.
Generated using https://github.com/ashleyzhou972/bioMRF.

Glossary: 
 - PhiMRF data: input data needed for PhiMRF, adjacency matrix and count matrix, in rds format.
 - PhiMRF results: output data from PhiMRF, list of posterior distributions, in rds format.
 - See https://github.com/ashleyzhou972/PhiMRF for details


Directory:

-- | IMR90_10kb_rnaseq.tar.gz
-- | -- | ENCFF353SBP.tsv : Raw RNA-seq quantification file from ENCODE
-- | -- | ENCFF496RIW.tsv : Raw RNA-seq quantification file from ENCODE
-- | -- | rnaseq_ENCFF353SBP.txt : Processed RNA-seq file
-- | -- | rnaseq_ENCFF496RIW.txt : Processed RNA-seq file
-- | -- | gene_names : Folder of gene names saved in rds format, by chromosome

-- | IMR90_10kb_intra.tar.gz
-- | -- | norm : Folder of normalized HiC counts mapped to gene, by chromosome
-- | -- | genepairs : Folder of normalized HiC count collapsed by gene pair, by chromosome
-- | -- | info : Folder of network info saved in rds format, by chromosome
-- | -- | linear : Folder of PhiMRF data saved in rds format, for linear gene networks, by chromosome
-- | -- | data : Folder of PhiMRF data saved in rds format, for linear gene networks, by chromosome
-- | -- | results : Folder of PhiMRF results, for four summary statistics, by chromosome

-- | IMR90_10kb_inter.tar.gz
-- | -- | norm : Folder of normalized HiC counts mapped to gene, by chromosome pair
-- | -- | genepairs : Folder of normalized HiC count collapsed by gene pair, by chromosome pair
-- | -- | info : Folder of network info saved in rds format, by chromosome pair
-- | -- | data : Folder of PhiMRF data saved in rds format, by chromosome pair
-- | -- | results : Folder of PhiMRF results, by chromosome pair

-- | IMR90_10kb_wholeGenome.tar.gz
-- | -- | all_data : Folder of PhiMRF data saved in rds format, for the combined (intra- and inter-) data of the whole genome

-- | IMR90_10kb_TADs.tar.gz
-- | -- | data 
-- | -- | -- | all_edges : Folder of PhiMRF data saved in rds format, for TAD genes, by chromosome
-- | -- | -- | intra_edges : Folder of PhiMRF data saved in rds format, for TAD genes, and intra-TAD edges, by chromosome
-- | -- | -- | inter_edges : Folder of PhiMRF data saved in rds format, for TAD genes, and inter-TAD edges, by chromosome
-- | -- | results 
-- | -- | -- | all_edges : Folder of PhiMRF results, for TAD genes, by chromosome
-- | -- | -- | intra_edges : Folder of PhiMRF results, for TAD genes, and intra-TAD edges, by chromosome
-- | -- | -- | inter_edges : Folder of PhiMRF results, for TAD genes, and inter-TAD edges, by chromosome

-- | IMR90_10kb_functional.tar.gz
-- | -- | data 
-- | -- | -- | GO:0000122_False_data : Folder of PhiMRF data saved in rds format, for genes annotated with GO:0000122, not propagated
-- | -- | -- | ... (18 folders ommited)
-- | -- | -- | GO:0045944_False_data : Folder of PhiMRF data saved in rds format, for genes annotated with GO:0045944, not propagated
-- | -- | results 
-- | -- | -- | ret_GO:0000122_False.rds : PhiMRF results, for genes annotated with GO:0000122, not propagated
-- | -- | -- | ... (18 files ommited)
-- | -- | -- | ret_GO:0045944_False.rds : PhiMRF results, for genes annotated with GO:0045944, not propagated

-- | IMR90_10kb_sheets.tar.gz
-- | -- | intra_all_mean_table3.csv : Parameter estimates (mean, 95% credible interval), using mean as summary, by chromosome  
-- | -- | intra_all_max_table3.csv : Parameter estimates (mean, 95% credible interval), using max as summary, by chromosome
-- | -- | intra_all_median_table3.csv : Parameter estimates (mean, 95\% credible interval), using median as summary, by chromosome             
-- | -- | intra_all_min_table3.csv : Parameter estimates (mean, 95% credible interval), using min as summary, by chromosome
-- | -- | linear_all_table3.csv :  Parameter estimates (mean, 95% credible interval), of all linear networks, by chromosome
-- | -- | inter_pair_all_table3.csv : Parameter estimates (mean, 95\% credible interval), by chromosome pair  
-- | -- | TADs_eta_table.csv : Parameter estimates (mean, 95\% credible interval) of TAD genes, by chromosome  
-- | -- | TADs_intra_eta_table.csv : Parameter estimates (mean, 95\% credible interval) of TAD genes, and intra-TAD edges, by chromosome
-- | -- | TADs_inter_eta_table.csv : Parameter estimates (mean, 95\% credible interval) of TAD genes, and inter-TAD edges, by chromosome
-- | -- | functional_nopropagate_all_table3.csv : Parameter estimates (mean, 95\% credible interval) of functional genes

-- | GM12878_10kb_rnaseq.tar.gz
-- | -- | ENCFF680ZFZ.tsv : Raw RNA-seq quantification file from ENCODE
-- | -- | ENCFF781YWT : Raw RNA-seq quantification file from ENCODE
-- | -- | rnaseq_ENCFF680ZFZ.txt : Processed RNA-seq file
-- | -- | rnaseq_ENCFF781YWT.txt : Processed RNA-seq file
-- | -- | gene_names : Folder of gene names saved in rds format, by chromosome

-- | GM12878_10kb_intra.tar.gz
-- | -- | norm : Folder of normalized HiC counts mapped to gene, by chromosome
-- | -- | genepairs : Folder of normalized HiC count collapsed by gene pair, by chromosome
-- | -- | info : Folder of network info saved in rds format, by chromosome
-- | -- | linear : Folder of PhiMRF data saved in rds format, for linear gene networks, by chromosome
-- | -- | data : Folder of PhiMRF data saved in rds format, for linear gene networks, by chromosome
-- | -- | results : Folder of PhiMRF results, for four summary statistics, by chromosome

-- | GM12878_10kb_inter.tar.gz
-- | -- | norm : Folder of normalized HiC counts mapped to gene, by chromosome pair
-- | -- | genepairs : Folder of normalized HiC count collapsed by gene pair, by chromosome pair
-- | -- | info: Folder of network info saved in rds format, by chromosome pair
-- | -- | data Folder of PhiMRF data saved in rds format, by chromosome pair
-- | -- | results: Folder of PhiMRF results, by chromosome pair

-- | GM12878_10kb_wholeGenome.tar.gz
-- | -- | all_data : Folder of PhiMRF data saved in rds format, for the combined (intra- and inter-) data of the whole genome

-- | GM12878_10kb_sheets.tar.gz
-- | -- | intra_all_table3.csv : Parameter estimates (mean, 95% credible interval), using mean as summary, by chromosome  
-- | -- | linear_all_table3.csv :  Parameter estimates (mean, 95% credible interval), of all linear networks, by chromosome
-- | -- | inter_pair_all_table3.csv : Parameter estimates (mean, 95\% credible interval), by chromosome pair