## ----style, echo = FALSE, results = 'asis'---------------------------------
BiocStyle::markdown()

## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE---------------------
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))
)
suppressPackageStartupMessages({
    library(Biostrings)
    library(GenomicRanges)
})

## ---- eval = FALSE---------------------------------------------------------
#  if (!require(BiocManager))
#      install.packages("BiocManager", repos = "https://cran.r-project.org")

## ---- eval = FALSE---------------------------------------------------------
#  BiocManager::install(c("Biostrings", "GenomicRanges"))

## ---- eval = FALSE---------------------------------------------------------
#  BiocManager::valid()

## ---- messages = FALSE-----------------------------------------------------
library(Biostrings)

## --------------------------------------------------------------------------
suppressPackageStartupMessages({
    library(GenomicRanges)
    library(GenomicAlignments)
})

## ---- eval = FALSE---------------------------------------------------------
#  vignette(package = "DESeq2")
#  browseVignettes("DESeq2")

## --------------------------------------------------------------------------
dir(system.file(package="DESeq2", "doc"))
vign <- system.file(package="DESeq2", "doc", "DESeq2.R")

## ---- eval = FALSE---------------------------------------------------------
#  source(vign, echo = TRUE, max.lines = Inf)

## ---- message = FALSE------------------------------------------------------
library(Biostrings)

## ----require---------------------------------------------------------------
library(GenomicRanges)

## ----help, eval=FALSE------------------------------------------------------
#  help(package="GenomicRanges")
#  vignette(package="GenomicRanges")
#  vignette(package="GenomicRanges", "GenomicRangesHOWTOs")
#  ?GRanges

## --------------------------------------------------------------------------
sessionInfo()