├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── chrAnalysis.R ├── chr_analysis.R ├── chr_order.R ├── color_sample.R ├── createVCFplot.R ├── geneAnalysis.R ├── get_chr_num.R ├── get_chr_plot_step.R ├── gt_null.R ├── load_chr.R ├── load_vcf.R ├── make_plot.R ├── model_vcf.R ├── read_vcf.R ├── snp_indel.R ├── spike_analysis.R └── vcf_genes.R ├── README.md ├── data-raw ├── GENE_RANGES.R ├── HG37_SEQINFO.R ├── HG38_CODING.R └── HG38_SEQINFO.R ├── data ├── EXONS37.rda ├── EXONS38.rda ├── GENES37.rda ├── GENES38.rda ├── HG37_SEQINFO.rda ├── HG38_CODING_CHR_DB.rda └── HG38_SEQINFO.rda ├── inst └── extdata │ ├── exampleVCF.vcf.gz │ └── exampleVCF.vcf.gz.tbi ├── man ├── adapt_color_sample.Rd ├── chrAnalysis.Rd ├── chr_analysis.Rd ├── chr_order.Rd ├── createVCFplot.Rd ├── geneAnalysis.Rd ├── get_chr_num.Rd ├── get_chr_plot_step.Rd ├── gt_null.Rd ├── load_chr.Rd ├── load_vcf.Rd ├── make_plot.Rd ├── model_vcf.Rd ├── read_vcf.Rd ├── snp_indel.Rd ├── spike_analysis.Rd └── vcf_genes.Rd └── plots ├── plotVCF.base.png ├── plotVCF.chr-wise.color.png ├── plotVCF.chr-wise.lencod.png ├── plotVCF.chr-wise.png ├── plotVCF.chr-wise.type.png ├── plotVCF.exon.png ├── plotVCF.flag-AF.png ├── plotVCF.flag-focus.png ├── plotVCF.flag-spaceline.png ├── plotVCF.flag-threshold-ylim.png ├── plotVCF.flag-threshold.png ├── plotVCF.flag.png ├── plotVCF.gene-wise.centile.png ├── plotVCF.gene-wise.color.png ├── plotVCF.gene-wise.png ├── plotVCF.gene.png ├── plotVCF.ordered.png ├── plotVCF.sample-focused-group.png ├── plotVCF.sample-focused-shape.png └── plotVCF.sample-focused.png /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^data-raw 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cccnrc/plot-VCF/HEAD/.gitignore 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