## ----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) }) ## ----dir, eval=TRUE, echo=FALSE, out.width="100%", fig.align = "center", fig.cap= "*systemPipeR's* preconfigured directory structure."---- knitr::include_graphics(system.file("extdata/images", "spr_project.png", package = "systemPipeR")) ## ----genRna_workflow_single, eval=FALSE--------------------------------------- # library(systemPipeRdata) # genWorkenvir(workflow="rnaseq") # setwd("rnaseq") ## ----project_rnaseq, eval=FALSE----------------------------------------------- # sal <- SPRproject() # sal <- importWF(sal, file_path = "systemPipeRNAseq.Rmd", verbose = FALSE) ## ----run_rnaseq, eval=FALSE--------------------------------------------------- # sal <- runWF(sal) ## ----plot_rnaseq, eval=FALSE-------------------------------------------------- # plotWF(sal) ## ----report_rnaseq, eval=FALSE------------------------------------------------ # sal <- renderReport(sal) # sal <- renderLogs(sal) ## ----genChip_workflow, eval=FALSE--------------------------------------------- # library(systemPipeRdata) # genWorkenvir(workflow="chipseq") # setwd("chipseq") ## ----project_chipseq, eval=FALSE---------------------------------------------- # sal <- SPRproject() # sal <- importWF(sal, file_path = "systemPipeChIPseq.Rmd", verbose = FALSE) ## ----run_chipseq, eval=FALSE-------------------------------------------------- # sal <- runWF(sal) ## ----plot_chipseq, eval=FALSE------------------------------------------------- # plotWF(sal) ## ----report_chipseq, eval=FALSE----------------------------------------------- # sal <- renderReport(sal) # sal <- renderLogs(sal) ## ----genVar_workflow_single, eval=FALSE--------------------------------------- # library(systemPipeRdata) # genWorkenvir(workflow="varseq") # setwd("varseq") ## ----project_varseq, eval=FALSE----------------------------------------------- # sal <- SPRproject() # sal <- importWF(sal, file_path = "systemPipeVARseq.Rmd", verbose = FALSE) ## ----run_varseq, eval=FALSE--------------------------------------------------- # sal <- runWF(sal) ## ----plot_varseq, eval=FALSE-------------------------------------------------- # plotWF(sal) ## ----report_varseq, eval=FALSE------------------------------------------------ # sal <- renderReport(sal) # sal <- renderLogs(sal) ## ----genRibo_workflow_single, eval=FALSE-------------------------------------- # library(systemPipeRdata) # genWorkenvir(workflow="riboseq") # setwd("riboseq") ## ----project_riboseq, eval=FALSE---------------------------------------------- # sal <- SPRproject() # sal <- importWF(sal, file_path = "systemPipeRIBOseq.Rmd", verbose = FALSE) ## ----run_riboseq, eval=FALSE-------------------------------------------------- # sal <- runWF(sal) ## ----plot_riboseq, eval=FALSE------------------------------------------------- # plotWF(sal) ## ----report_riboseq, eval=FALSE----------------------------------------------- # sal <- renderReport(sal) # sal <- renderLogs(sal) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()