Course Overview


Course Integrity

This course is compiled automatically on 2025-06-11
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The course is tested and available on MacOS, Windows and Ubuntu Linux for R version 4.4.0 (2024-04-24)
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Overview

This course consists of 6 sections, walking participants through the basic concepts in analyzing epigenomic data: Sequencing QC, Alignment, Peak Calling, Technique Specific QC, Differentials, Annotation and Motif Analysis.

Each section is presented as HTMl presentations or single page document. Exercises and answer sheets are included after all subsections to practice techniques and provide future reference examples

Course material and exercises are available to view as rendered HTML at https://rockefelleruniversity.github.io/RU_Course_template/.

All material is available to download under GPL v2 license.



Setting up


System Requirements

Install MACS3

Though there is a R package for MACS, we typically use MACS3 from the Anaconda package repository for Linux or MacOS. The easiest way to install MACS3 is using the R package Herper. Herper allows you to manage and install Anaconda packages from within R.

BiocManager::install("Herper")
library(Herper)

Once Herper is installed you can install MACS3 with the install_CondaTools function. Behind the scenes, Herper will install the most minimal version of conda (called miniconda), and then will create a new environment into which MACS3 will be installed. When you run the function it prints out where MACS3 is installed.

The env argument is the name you want to give the environment created. The pathToMiniConda specifies the location you want to install Miniconda, and all the conda tools like MACS2.

install_CondaTools(tools="macs3", env="PeakCalling_analysis", pathToMiniConda="/path/to/install")

More information on MACS3 is available from the Tao Liu’s dedicated GitHub page.


Install MEME

There is no R package for MEME, but MEME is available in the Anaconda package repository for Linux or MacOS. The easiest way to install MEME is using the R package Herper. Herper allows you to manage and install Anaconda packages from within R.

BiocManager::install("Herper")
library(Herper)

Once Herper is installed you can install MEME with the install_CondaTools function. Behind the scenes, Herper will install the most minimal version of conda (called miniconda), and then will create a new environment into which MEME will be installed. When you run the function it prints out where MEME is installed.

The env argument is the name you want to give the environment created. The pathToMiniConda specifies the location you want to install Miniconda, and all the conda tools like MEME.

install_CondaTools(tools="meme", env="Motif_analysis", pathToMiniConda="/path/to/install", channels="bioconda")

More information on MEME can be found on the website.


Install R

R can be installed from the R-project website.

The R website can be found here http://www.r-project.org/. This website has all the latest information about R updates, conferences and installation

You can use this direct links to the install for each major OS:


Install RStudio

RStudio can be installed from the RStudio website.

http://www.rstudio.com/

RStudio can be downloaded for all platforms at the link below

https://rstudio.com/products/rstudio/download/


Install SEACR

There is no R package for SEACR, but you can download it from the Fred Hutch GitHub page.

You will need to unzip it and then you should be good to go. Here are the commands to do this all in R.

download.file("https://github.com/FredHutch/SEACR/archive/refs/tags/v1.4-beta.2.zip", destfile = "~/Downloads/SEACR_v1.4.zip")
unzip("~/Downloads/SEACR_v1.4.zip", exdir = "~/Downloads/SEACR_v1.4" )
seacr_path <- "~/Downloads/SEACR_v1.4/SEACR-1.4-beta.2/SEACR_1.4.sh"

To test SEACR is running correctly you can run the SEACR help command from R.

system(paste(seacr_path, "-h"))

Some people get an error message at this stage as SEACR does not have permission to run. You can update your permissions like this.

system(paste("chmod 777", seacr_path))
system(paste(seacr_path, "-h"))

More information on SEACR is available on the GitHub page along with the SEACR website (which also includes a web interface for running SEACR).


Install required R packages

R Packages can be installed from the course package or from CRAN/Bioconductor. These commands should be written into the R console. Once R and RStudio is installed, you can copy and paste these install commands into lower left pane of RStudio which should be labelled “Console”. If you run into any errors, do this one line at a time.

From the course package
install.packages('BiocManager')
install.packages('remotes')
BiocManager::install('RockefellerUniversity/ATAC.Cut-Run.ChIP',subdir='ATACCutRunChIP')
From CRAN and Bioconductor
install.packages('BiocManager')
BiocManager::install('methods')
BiocManager::install('ggplot2')
BiocManager::install('rmarkdown')
BiocManager::install('rio')
BiocManager::install('ShortRead')
BiocManager::install('Rfastp')
BiocManager::install('msigdbr')
BiocManager::install('ggupset')
BiocManager::install('BSgenome.Mmusculus.UCSC.mm10')
BiocManager::install('Rsubread')
BiocManager::install('Rsamtools')
BiocManager::install('rtracklayer')
BiocManager::install('Herper')
BiocManager::install('GenomicAlignments')
BiocManager::install('ChIPQC')
BiocManager::install('ATACseqQC')
BiocManager::install('soGGi')
BiocManager::install('limma')
BiocManager::install('DESeq2')
BiocManager::install('tracktables')
BiocManager::install('TxDb.Mmusculus.UCSC.mm10.knownGene')
BiocManager::install('EnhancedVolcano')
BiocManager::install('clusterProfiler')
BiocManager::install('rGREAT')
BiocManager::install('org.Mm.eg.db')
BiocManager::install('GenomeInfoDb')
BiocManager::install('motifmatchr')
BiocManager::install('memes')
BiocManager::install('ChIPseeker')
BiocManager::install('enrichplot')
BiocManager::install('MotifDb')
BiocManager::install('JASPAR2024')
BiocManager::install('RSQLite')
BiocManager::install('TFBSTools')
BiocManager::install('seqLogo')
BiocManager::install('ggseqlogo')
BiocManager::install('universalmotif')
BiocManager::install('Biostrings')
BiocManager::install('knitr')
BiocManager::install('testthat')
BiocManager::install('yaml')

Download the material

Download the material




The Presentations


Epigenomics , Session 1

This section focuses on sequencing QC

  • Introduction to different epigenomic techniques
  • Sequencing QC

Epigenomics , Session 2

This section focuses on alignment and peak calling

  • How to build a reference genome index
  • Running alignment
  • Peak calling with MACS and SEACR

Epigenomics , Session 3

This section focuses on technique-specific QC

  • Cut&Run and ChIP QC with the ChIPQC package
  • ATAC QC with the ATACseqQC package

Epigenomics , Session 4

This section focuses on differentials peak analysis

  • Peak intersections and unique peaks
  • Generating a consensus
  • Using DESeq2 to run differentials

Epigenomics , Session 5

This section focuses on annotation of peaks and functional enrichment analysis

  • Annotate peaks to genomic features
  • Annotate peaks to genes
  • Perform gene and region centric functional enrichment

Epigenomics , Session 6

This section focuses on motif analysis

  • Motif databases and making seqlogos
  • Motif enrichment analysis with MEME
  • De novo motif analysis with MEME
  • Finding motifs with motifmatchr

Getting help


Course help

For advice, help and comments for the material covered in this course please contact us at the issues page associated to this course.

The link to the help pages can be found here


General Bioinformatics support

If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at .