ATACseeker App

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