CCGA_circulome

This repository contains code from "Lv et al. Chromosomal, Extrachromosomal, and Transcriptomic Alternation Landscape in Urothelial Bladder Carcinoma".

Code

mutations

• Annovar2MAF.pl
• CombineVariant.pl

obtain GC contents

• calGC.py
• calGC.sh

obtain repeat ratios

• calReps.sh
• calReps.py

some basic statistics

• calMappings_nochrM.py obtain total mapping reads for each sample except chrM
• get_index_statistic.py obtain total mapping ratio for each chromosome
• filter.py filter raw eccDNA using some metrics
• start_anno.jl annotate eccDNA usings their start junction
• run_GISTIC2.sh analyze total CNA characters from all samples
• getBreaks.jl obtain all discordant break points from ecDNA graphs
• PABPC1_CIRCLE_RNA_WGS_alleleCount.sh example for allelic frequency and coverage

scripts for main figure plots

• MutationFreq.Sel.R

• Stat_Kataegis_WithinEvents_or_10k.R

• TMB_MSig.R

• TumorVAF_Kataegis_Kyklonas.R

• TumorVAF_Kyklonas_Oncogene.R

• UBC_SBS.R

• UBC_SBS_exposure_PCT_kmeans.R

• UBC_enrichment_MSig.R

• UBC_lollipopPlot_FGFR3_ecDNA.R

• UBC_lollipopPlot_KDM6A.R

• UBC_lollipopPlot_KMT2D.R

• UBC_lollipopPlot_TP53.R

• UBC_lollipopPlot_TTN_ecDNA.R

• UBC_mafSurvival.R

• UBC_oncoplot.R

• UBC_rainfallPlot-Selected.R

• UBC_survival_OS_MSig.R

• UBC_survival_PFS_MSig.R

• UBC_tcgaCompare.R

• annotate_eccDNA_elements.plotData.R

• B-allele_WGS_CircleSeq.plot.R

• classify_samples_ecDNA.plotData.R

• compare_eccDNA_abundance_heatmap.plot.R

• compare_ecDNA_size_copy_BP.plotData.R

• compare_EPM.plot.R

• detected_chimeric_eccDNA.plotData.R

• ecc_abundance_distribution.plot.R

• ecc_map_genes.plotData.R

• ecc_mRNA_cor.plot.R

• ecc_mRNA_cor_rank.plot.R

• eccNumbers_amp_noamp.plotData.R

• EPM_diff_GSEA.plot.R

• epm_mRNA_cor.plot.R

• foldchange_amp_noamp.plot.R

• genomic_dotplot_allele_frequency.plot.R

• length_category_compare.plotData.R

• length_distribution_eccDNA.plot.R

• ligation_genes_exp_cor.plot.R

• mRNA_ecDNA_eccDNA.plot.R

• multiomicsViz.plot.R

• oncoprint_for_BLCA_UBC.plot.R

• PABPC1_circle_coverage.plot.R

• statistic_for_BLCA_proportion.plotData.R

SV format and merge

• format_delly.jl
• format_manta.jl
• merge.manta.delly.py

Contact

If you have any questions concerning code or data, please do not hesitate to contact us at panxiaoguang@genomics.cn or/and huangjinrong@genomics.cn.