├── .gitignore ├── .gitmodules ├── LICENSE ├── Makefile ├── R ├── chromVAR.R ├── dpeaks.R ├── karyoplot.R ├── metrics.R └── variance.R ├── README.md ├── bed ├── promoter.R └── wgEncodeDacMapabilityConsensusExcludable.bed.gz ├── doc ├── .gitignore ├── Makefile ├── README.md ├── _bookdown.yml ├── atac.Rmd ├── index.Rmd ├── preprocess.sh ├── requirements.sh └── sample.mapping ├── docker └── Dockerfile ├── example └── example.sh ├── motif └── downloadMotifs.sh ├── src ├── align.sh ├── atac.sh ├── count.sh ├── footprints.sh ├── homer.sh ├── motif.sh ├── pdx.sh ├── peaks.sh ├── pseudorep.sh ├── qc_globber.py ├── qc_globber.sh └── variants.sh └── tracks └── downloadTracks.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tobiasrausch/ATACseq/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: 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