Workshop on Epigenomics data analysis - June/July22
Section outline
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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. -
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