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.
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
RStudio can be installed from the RStudio website.
RStudio can be downloaded for all platforms at the link below
https://rstudio.com/products/rstudio/download/
install.packages('BiocManager')
BiocManager::install('RockefellerUniversity/Genomic_HeatmapsAndProfiles',subdir='GenomicHeatmaps')
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')
In this session we introduce plotting using Deeptools and Profileplyr.
Session sections:
The html slide presentation can be found at this link Slide
The single page html presentation can be found at this link Single Page
The code use in the presentations can be found at R code
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
If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at brc@rockefeller.edu.