├── ChIP-seq ├── plot │ ├── ChIPseqPlot.R │ ├── ChIPseqPlot.brief.r │ ├── ChIPseqPlot_V1.3.py │ ├── nohup.out │ ├── plot.public.tss.sh │ ├── plot.sh │ └── plot.tss.sh └── pre-process │ ├── bdg2bw.sh │ ├── idxstats.sh │ ├── index_batch.sh │ ├── step1_clean_batch.sh │ ├── step2_align_batch.sh │ ├── step3_rmd_batch.sh │ ├── step5_macs2_CTCF.sh │ ├── step5_macs2_DNase.sh │ ├── step5_macs2_batch.sh │ ├── step6_bdg2bw.sh │ ├── step7_deeptools_bam2bw.sh │ ├── step7_deeptools_bam2bw_CP.sh │ ├── step8_homer_maketag.pl │ └── step9_homer_findPeaks.pl ├── HiC-preprocess ├── compartments │ ├── callAB.R │ ├── compareAB.R │ ├── compareAB.ourvspublic.R │ ├── compare_AB_500kb.r │ ├── cor_AB_genomicfeatures.R │ ├── find_AB_continusRegion.R │ ├── plot.pearsoncor.heatmap.R │ ├── plotAB.pearsoncor.R │ ├── plot_AB_chrom.r │ ├── plot_OE_matrix.R │ └── plotheatmap.public.cellline.R ├── loop │ ├── APA.monkey.CP.sh │ ├── calculate_map_resolution.sh │ ├── diffloop.sh │ ├── dump.sh │ ├── hicpro2juicebox_cw.sh │ ├── loop.batch.pl │ ├── loopcp.sh │ ├── loopgz.sh │ ├── pre-cp.sh │ └── pre-gz.sh └── tad │ ├── Boundary2TAD │ ├── boundary.txt │ ├── createTAD.pl │ ├── filterGap.pl │ ├── rheMac8.chrom.sizes.brief │ └── rheMac8.contig.hgTable.txt │ ├── DomainCaller-Renlab │ ├── DI_from_matrix.sh │ ├── concatenate_DI.sh │ ├── domain.sh │ ├── hmm_7col.sh │ └── split_7col.sh │ ├── insulation.sh │ └── permit_for_insulationsocre.R └── RNA-seq ├── QC-GOplot ├── Orth_step1_featureCounts.R ├── Orth_step1_featureCounts_rh.R ├── Orth_step2_cluster.R ├── Orth_step3_DE.R ├── Orth_step4_compare_withpublic.R ├── ensemble_Mmu8_gene_GC_lengths.txt ├── step0_genename2id.R ├── step0_gtf_genelocation.R ├── step1_select_orthologs.R ├── step2_cluster.R ├── step2_cluster_Rh.R ├── step2_cluster_Rh_FPKM.R ├── step3_FPKM_cqn_normalize.R ├── step4_combat_batcheffect_FPKM.R ├── step5_DE.R ├── step5_DE_Rh.R ├── step6_comparewithpublic.R ├── step7_selectgene_boxplot.R ├── step8_geneFC.R └── step9_GOterm_barplot.R ├── XSAnno ├── 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