## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() options(width=80, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), tidy.opts=list(width.cutoff=80), tidy=TRUE) ## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE------------------------ suppressPackageStartupMessages({ library(systemPipeR) library(BiocParallel) library(Biostrings) library(Rsamtools) library(GenomicRanges) library(ggplot2) library(GenomicAlignments) library(ShortRead) library(ape) library(batchtools) }) ## ----genRna_workflow_single, eval=FALSE--------------------------------------- # library(systemPipeRdata) # genWorkenvir(workflow="rnaseq") # setwd("rnaseq") ## ----genChip_workflow, eval=FALSE--------------------------------------------- # library(systemPipeRdata) # genWorkenvir(workflow="chipseq") # setwd("chipseq") ## ----genVar_workflow_single, eval=FALSE--------------------------------------- # library(systemPipeRdata) # genWorkenvir(workflow="varseq") # setwd("varseq") ## ----genRibo_workflow_single, eval=FALSE-------------------------------------- # library(systemPipeRdata) # genWorkenvir(workflow="riboseq") # setwd("riboseq") ## ----sessionInfo-------------------------------------------------------------- sessionInfo()