This repository contains code for a Illumina BaseSpace Native App for doing ATACseq analysis.
requires:
- docker, pandoc, parallel
- bamaddrg, bedtools, bedGraphToBigWig, bwa, freeBayes, samblaster, samtools, vcftools, vcflib
- R
- Bioconductor: csaw, edgeR, Gviz, Homo.sapiens, preseqR, Rsamtools, rtracklayer
- CRAN: knitr, locfit, R2HTML, rjson, rmarkdown, statmod
- Github: ATACseeker