├── .gitattributes ├── Data ├── CRInfo_human.mat ├── CRInfo_mouse.mat ├── MotifMatch_human_rmdup.mat ├── MotifMatch_mouse_rmdup.mat ├── Motif_TF_human.txt ├── Motif_TF_mouse.txt ├── TFName_human.txt ├── TFName_mouse.txt ├── TFTG_human_nagetriveControl.mat ├── TFTG_mouse_nagetriveControl.mat ├── all_motif_rmdup ├── genome_100k_hg19.bed ├── genome_100k_hg38.bed ├── genome_100k_mm10.bed ├── genome_100k_mm9.bed ├── promoter_hg19.bed ├── promoter_hg38.bed ├── promoter_mm10.bed └── promoter_mm9.bed ├── Input ├── RAd4.bam ├── RAd4.bam.bai └── RAd4.txt ├── PECA 2.0 manual v3.3.pdf ├── PECA.sh ├── PECA_compare_dif.sh ├── PECA_compare_dif_multiple.sh ├── PECA_compare_withoutENCODE.sh ├── PECA_multi.sh ├── PECA_withoutENCODE.sh ├── Prior ├── Enhancer_RE_gene_corr_hg19.bed ├── Enhancer_RE_gene_corr_hg38.bed ├── Enhancer_RE_gene_corr_mm10.bed ├── Enhancer_RE_gene_corr_mm9.bed ├── Opn_median_hg19.bed ├── Opn_median_hg38.bed ├── Opn_median_mm10.bed ├── Opn_median_mm9.bed ├── RE_gene_corr_hg19.bed ├── RE_gene_corr_hg38.bed ├── RE_gene_corr_mm10.bed ├── RE_gene_corr_mm9.bed ├── TFTG_corr_human.mat └── TFTG_corr_mouse.mat ├── README.md ├── comparative_regulatory_analysis.md ├── install.sh ├── scr ├── FindSubNetwork_bi1.m ├── FindSubNetwork_bi2.m ├── PECA_dif_net.m ├── PECA_dif_net_multiple.m ├── PECA_network_hg19.m ├── PECA_network_hg38.m ├── PECA_network_mm10.m ├── PECA_network_mm9.m ├── compareNet.m ├── dif_test.m ├── mf_collect.m ├── mfbs.m └── prior_calculation.m └── tutorial.md /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SUwonglab/PECA/HEAD/.gitattributes -------------------------------------------------------------------------------- /Data/CRInfo_human.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SUwonglab/PECA/HEAD/Data/CRInfo_human.mat -------------------------------------------------------------------------------- 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