Section 1 Setup

1.1 Installation

devtools::install_github(repo = "knausb/vcfR")  # removed from CRAN
devtools::install_github("jokergoo/ComplexHeatmap")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("rtracklayer")
install.packages("rmdformats")
install.packages("ggplot2")
install.packages("reshape2")
install.packages("ggridges")
install.packages("data.table")
install.packages("knitr")
install.packages("kableExtra")
install.packages("plotly")
install.packages("DT")
install.packages("circlize")
install.packages("ComplexHeatmap")
install.packages("rtracklayer")
install.packages("bookdown")
install.packages("XML")
install.packages("randomcoloR")
install.packages("ggrepel")
devtools::install_github(repo = "omegahat/XML")  # needs `brew install libxml2` on macos
rm(list = ls())
source("utils.R")
library("vcfR")
library("rmdformats")
library("ggplot2")
library("reshape2")
library("ggridges")
library("data.table")
library("knitr")
library("kableExtra")
library("plotly")
library("DT")
library("circlize")
library("ComplexHeatmap")
library("rtracklayer")
library("ggrepel")
library("randomcoloR")
library("bookdown")
library("HaplotypeDeconstructor")
library("NMF")
source("nmf_functions.R")

1.2 Generate report

setwd("~/ActiveProjects/OligoMM-report")
bookdown::serve_book(getwd())

Note: for rtracklayer you might need curl

sudo apt-get install libcurl4-openssl-dev

You need to install Pandoc.

servr::daemon_stop(1)

This will starts a browser window pointing to http://127.0.0.1:7853 presenting the report written in R Markdown and will update as soon as there are changes on .Rmd files in the workspace.