├── CNV GISTIC analysis └── run_gistic.sh ├── RNA methylation correlation analysis ├── 01_mRNA_WGBS_cor.r ├── 02_pie_CGI.r ├── 03_TSS_around.py ├── 04_cluster_heatmap.R └── 05_phenotype_CIMP.r ├── RNA-seq data processing ├── 01_summary_rna_metrics.R ├── 01_trimAdapter.sh ├── 02_gene_exp_mat.R ├── 02_mapping.sh ├── 03_DEG_edgeR.R ├── 03_quantification.sh ├── 04_DEG_edgeR.sh └── 04_GoKegg_clusterProfiler_hs.R ├── TME analysis ├── 01_TME-deconv.R └── 02_integrate immune therapy samples and 155 cohort.R ├── WGBS data processing ├── 01_region.methylation.pl ├── 01_trim_galore.bismark.sh ├── 02_enrich_WGBS.R ├── 02_metilene.CG.sh ├── 03_heatmap_circos.conf └── 04_2D_density.R ├── WGS data processing ├── 01_create_QCtable.py ├── 01_sentieon_variant_calling.sh ├── 02_cnvkit_process.sh ├── 02_vcf2anno.py └── 03_vcf2maf_mutsig.py ├── miRNA data processing ├── 01_clean_reads_stat.sh ├── 01_mirdeep_mapper.sh ├── 02_Rfam_blast_short.sh ├── 02_rfam_stat.R ├── 03_Mean_count.R ├── 03_mirdeep2_count.sh ├── 04_DEG_miRNA_edgeR.sh └── 04_miRNA_target_select.pl ├── multi-omics integrative analysis ├── 01_clustering on single platform data.R ├── 02_COCA.R ├── 03_muli-omics pathway plot.R └── 04_C2 expression methylation comparison.R └── mutational signature analysis └── signature.R /CNV GISTIC analysis/run_gistic.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CICAMS-Liu-lab/ECGEA/HEAD/CNV GISTIC analysis/run_gistic.sh -------------------------------------------------------------------------------- /RNA methylation correlation analysis/01_mRNA_WGBS_cor.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CICAMS-Liu-lab/ECGEA/HEAD/RNA methylation correlation analysis/01_mRNA_WGBS_cor.r -------------------------------------------------------------------------------- /RNA methylation correlation analysis/02_pie_CGI.r: 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