Course Overview


This course introduces plotting and importing Genomic Heatmaps in R.

The course consists of 1 sections on plotting and importing Genomic Heatmaps in R.
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_ATACseq/. All material is available to download under GPL v2 license.



Setting up


System Requirements

Install IGV

IGV can be installed from the BROAD website.

https://www.broadinstitute.org/igv/


Install R

R can be installed from the R-project website.

The R website can be found here http://www.r-project.org/.

The download links and associated installation instructions for multiple platforms can be found below provided by Revolution Analytics. https://cran.revolutionanalytics.com

Direct downloads for main platforms of R 4.0 can be found below


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 required packages

From the course package

install.packages('BiocManager')
BiocManager::install('RockefellerUniversity/Genomic_HeatmapsAndProfiles',subdir='GenomicHeatmaps')


From CRAN and Bioconductor

install.packages('BiocManager')
BiocManager::install('methods')
BiocManager::install('ggplot2')
BiocManager::install('rmarkdown')
BiocManager::install('ShortRead')
BiocManager::install('ashr')
BiocManager::install('ChIPQC')
BiocManager::install('DiffBind')
BiocManager::install('BSgenome.Hsapiens.UCSC.hg19')
BiocManager::install('Rsubread')
BiocManager::install('Rbowtie2')
BiocManager::install('R.utils')
BiocManager::install('Rsamtools')
BiocManager::install('BSgenome.Hsapiens.UCSC.hg38')
BiocManager::install('rtracklayer')
BiocManager::install('ChIPseeker')
BiocManager::install('soGGi')
BiocManager::install('GenomicAlignments')
BiocManager::install('TxDb.Hsapiens.UCSC.hg19.knownGene')
BiocManager::install('DESeq2')
BiocManager::install('BSgenome.Mmusculus.UCSC.mm10')
BiocManager::install('TxDb.Hsapiens.UCSC.hg38.knownGene')
BiocManager::install('TxDb.Mmusculus.UCSC.mm10.knownGene')
BiocManager::install('devtools')
BiocManager::install('profileplyr')
BiocManager::install('tidyr')
BiocManager::install('DT')
BiocManager::install('dplyr')
BiocManager::install('rGREAT')
BiocManager::install('MotifDb')
BiocManager::install('Biostrings')
BiocManager::install('GenomicRanges')
BiocManager::install('pheatmap')
BiocManager::install('org.Mm.eg.db')
BiocManager::install('knitr')
BiocManager::install('testthat')
BiocManager::install('yaml')


Download the material

Download the material




The Presentations


Genomic Heatmaps, Session 1

In this session we introduce plotting using Deeptools and Profileplyr.

Session sections:

  • Introduction to Genomic Heatmaps.
  • Importing Deeptools heatmaps into R.
  • Profileplyr package heatmaps plotting.

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 .