├── .gitignore ├── CITATION.cff ├── LICENSE ├── README.md ├── gather-fastqs ├── generate-settings ├── routes ├── atac.sh ├── chip-pairs-peaks.sh ├── chip.sh ├── rna-rsem.sh ├── rna-salmon.sh ├── rna-snv.sh ├── rna-star-groups-dge.sh ├── rna-star.sh ├── rrbs.sh ├── species.sh ├── wes-pairs-cnv.sh ├── wes-pairs-snv.sh ├── wes.sh └── wgbs.sh ├── run ├── scripts ├── deseq2-compare.R ├── deseq2-pca.R ├── dge-deseq2.R ├── fix-csv.sh ├── fragment-sizes.R ├── get-ref.sh ├── get-set-setting.sh ├── gse-fgsea.R ├── join-many.sh ├── load-install-packages.R ├── plot-heatmap.R ├── plot-volcano.R ├── quant-merge-salmon.R ├── test-package.R └── vcf-table.R └── segments ├── align-bismark.sh ├── align-bowtie2-atac.sh ├── align-bowtie2-chip.sh ├── align-bwa-mem.sh ├── align-star.sh ├── annot-annovar.sh ├── annot-regions-annovar.sh ├── bam-dedup-bismark.sh ├── bam-dedup-sambamba.sh ├── bam-ra-rc-gatk.sh ├── bam-splitncigar-gatk.sh ├── bigwig-bedtools.sh ├── bigwig-deeptools.sh ├── cnvs-wes-freec.sh ├── 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