Prerequisites

The course is intended for those who have been through a very basic introduction to Unix and the R scripting language.

If a refresher is needed for Unix command line, please go over this tutorial and its companion cheatsheet.
Another helpful UNIX cheatsheet: here
Getting down to basics: an introduction to the fundamentals of R (courtesy of Mark Ravinet).

Local configuration

A Docker image is available for this workshop:

You can get access to all the packages used in this book in < 1 minute, using this command in a terminal:

bash

docker run -it ghcr.io/js2264/ngs-physalia:devel R

Computer with high-speed internet access
Zoom visioconference software
For Windows users: PLEASE INSTALL WSL 2. Instructions are here: learn.microsoft.com/en-us/windows/wsl/install
IGV software installed
Several system dependencies
- R>=4.1
- fastqc
- cutadapt
- trim_galore
- bowtie2
- deepTools
- macs2
- meme
- subread

Installing system dependencies with micromamba

micromamba is a blazing-fast flavour of conda, a software manager available in Mac and Linux. micromamba sets up environments, directories in your computer in which micromamba installs softwares only available upon environment activation.

To install micromamba and system dependencies listed hereabove, use the following:

sh

# apt update && apt install -y bzip2 curl wget
curl -L micro.mamba.pm/install.sh | bash
bash
micromamba create -n epigenomics
micromamba install --name epigenomics -c bioconda -c conda-forge \
    fastqc fastqc trim-galore bowtie2 deepTools macs2 meme subread star samtools bedtools \
    pandas numpydoc matplotlib cooler cooltools hicstuff

Several R packages, the main ones being:
- BiocManager
- SummarizedExperiment
- rtracklayer
- GenomicRanges
- GenomicAlignments
- GenomicFeatures
- DESeq2
- gprofiler2