Topic outline

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  General

  Workshop on Epigenomics data analysis

  30 June - 1 July 2022, Centre de conférences et de séminaires, Caux Palace / Montreux
  

  
  

  Course schedule

  Program: Day 1: June 30th 9h00-12h30 / 13h30-17h00 . 9h00 - 9h30 : General introduction to the data for epigenomics . 9h30 - 10h45 : Prokaryotic DNA methylation (PacBio, etc.) (Laurent Falquet) . Coffee break 10h45-11h . 11h00 - 12h30: Prokaryotic DNA methylation: hands-on (Laurent Falquet) . 12h30 - 13h30: lunch break . 13h30 - 14h30: Eukaryotic DNA methylation (bisulfite sequencing and/or EMseq) (Mario Iurlaro) . 14h30 - 14h40: short break . 14h40 - 17h00 : Eukaryotic DNA methylation: hands-on (Mario Iurlaro) with a coffe break in the middle. Day 2: July 1st / 9h00-12h30 / 13h30-17h00 . 09h00 - 10h00: Histone modification and chromatine re-arrangement (Guido Van Mierlo) . 10h00 - 12h30: Histone modification and chromatine re-arrangement: Hand-on. with Coffee break around 10h40. . 12h30 - 13h30: Lunch break . 13h30 - 17h00 : Cancer epigenomics: data visualization (Philipp Bucher), lectures + hands-on with Coffee break 15h20-15h40

  
  

  Requirements: a Mac or PC with RStudio installed.

  
  
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  instructions

  Day 1 - Session 1 

  BEFORE arrival, please install RStudio on your laptop (Mac or PC) and within RStudio install the following packages:

  install.packages("ggplot2") 

  if (!require("BiocManager", quietly = TRUE))  install.packages("BiocManager")

  BiocManager::install("Biostrings")
  

  On your laptop 

  1) download on your desktop the file given the link below https://drive.switch.ch/index.php/s/OJclI29CcvR1th8
  2) gunzip and untar the file "prokaryotes.tar.gz"

  Follow the hands-on file below (Prokaryotes).

  
  

  Day 1 - Session 2
  

  Assuming BiocManager is already installed for previous session, then:

  BiocManager::install(c("QuasR","MethylSeekR","Gviz","BSgenome.Hsapiens.UCSC.hg18"))
  

  https://www.dropbox.com/s/8d00dy1h6nk602k/Bisseq_analysis_in_R.html?dl=0

  
  

  
  

  Day 2 - Session 1

  Please download the data and exercise from https://drive.switch.ch/index.php/s/vcARszUBLBXjZkX to your laptop. 

  Please install the following R packages:

  data.table (https://www.rdocumentation.org/packages/data.table/versions/1.14.2)

  dplyr (https://dplyr.tidyverse.org/). To be complete you can also directly install the whole tidyverse using: install.packages("tidyverse")

  tidyr (https://tidyr.tidyverse.org/). To be complete you can also directly install the whole tidyverse using: install.packages("tidyverse")
  

  ggplot2 (https://ggplot2.tidyverse.org/) (should be already installed from day 1 - session 1)
  

  ComplexHeatmap (https://www.bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html)

  ChIPseeker (https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html)

  clusterProfiler (https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html)

  TxDb.Hsapiens.UCSC.hg19.knownGene (https://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html)

  org.Hs.eg.db (https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html)

  edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html)
  
  GenomicRanges (https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html)
  
  

  Day 2 - Session 2
  

  • Day 1 - Session 1: for cut&paste in RStudio Page
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  Course slides & exercises