## ----bioconductor, eval=FALSE------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("nanotubes") ## ----library, results='hide', message=FALSE----------------------------------- library(nanotubes) ## ----github, eval=FALSE------------------------------------------------------- # devtools::install_github("MalteThodberg/nanotubes") ## ----citation, eval=TRUE------------------------------------------------------ citation("nanotubes") ## ----nanotubes---------------------------------------------------------------- data("nanotubes") knitr::kable(nanotubes) ## ----rtracklayer, message=FALSE----------------------------------------------- library(rtracklayer) bw_fname <- system.file("extdata", nanotubes$BigWigPlus[1], package = "nanotubes", mustWork = TRUE) import(bw_fname) ## ----CAGEfightR, eval=FALSE--------------------------------------------------- # library(CAGEfightR) # # # Setup paths # bw_plus <- system.file("extdata", nanotubes$BigWigPlus, # package = "nanotubes", # mustWork = TRUE) # bw_minus <- system.file("extdata", nanotubes$BigWigMinus, # package = "nanotubes", # mustWork = TRUE) # # # Save as named BigWigFileList # bw_plus <- BigWigFileList(bw_plus) # bw_minus <- BigWigFileList(bw_minus) # names(bw_plus) <- names(bw_minus) <- nanotubes$Name # # # Quantify # CTSSs <- quantifyCTSSs(bw_plus, bw_minus, design=nanotubes) ## ----session------------------------------------------------------------------ sessionInfo()