This page provides details and information about the Summer School. We will be updating the site, therefore, if you are attending review it before the course.
IMPORTANT: any updates, comments or additions will be highlighted in RED.
- SET YOUR COMPUTER READY.
Everyone is expected to bring a laptop to the course and have the following elements installed and/or downloaded.
a. R, https://www.r-project.org
Install R version 3.5.1
b. RStudio, https://www.rstudio.com
Install RStudio Desktop Version 1.1.456
c. R packages.
Install the following packages:
install.packages(“reshape”)
install.packages(“survival”)
install.packages(“ggplot2”)
install.packages(“ggfortify”)
install.packages(“VennDiagram”)
install.packages(“plotrix”)
install.packages(“MASS”)
install.packages(“gridExtra”)
install.packages(“igraph”)
install.packages(“BoolNet”)
install.packages(“multinets”)
install.packages(“metafor”)
install.packages(“metaviz”)
install.packages(“RobustRankAggreg”)
install.packages(“mvtmeta”)
Additionally, to install the Muxviz package you will need to download and install it from github: http://muxviz.net/
d. Bioconductor packages.
Install the following packages, from Bioconductor 3.7 (BiocInstaller 1.30.0)
source(“https://bioconductor.org/biocLite.R”)
biocLite(“IlluminaHumanMethylation450kanno.ilmn12.hg19”)
biocLite(“lumi”)
biocLite(“limma”)
biocLite(“sva”)
biocLite(“rtracklayer”)
biocLite(“biomaRt”)
biocLite(“NOISeq”)
biocLite(“cqn”)
biocLite(“sva”)
biocLite(“maSigPro”)
biocLite(“mdgsa”)
biocLite(“BiSeq”)
biocLite(“bsseq”)
biocLite(“bsseqData”)
biocLite(“methylKit”)
biocLite(“DART”)
biocLite(“FEM”)
biocLite(“GenomicRanges”)
biocLite(“SummarizedExperiment”)
biocLite(“parallel”)
biocLite(“IRanges”)
biocLite(“DART”)
biocLite(“FEM”)
Additionally, we require you to install resoruces on mm10
biocLite(c(“biomaRt”, “TxDb.Mmusculus.UCSC.mm10.knownGene”, “TxDb.Mmusculus.UCSC.mm10.ensGene”, “BSgenome.Mmusculus.UCSC.mm10”))
Additionally, we require you to install the developer version of STATegRa package, which is a package we are developing. Use the following commands
Step 1: install devtools: library(devtools)
Step 2: install developer version: install_github(“lunacab/STATegRa”)
Additionally, we require you to install the following packages for the single-cell data analysis.
biocLite(“scater”, quietly = TRUE)
biocLite(“scran”)
biocLite(“Seurat”)
biocLite(“gridExtra”)
biocLite(“ggpubr”)
biocLite(“biomaRt”)
biocLite(“GSEABase”)
biocLite(“org.Mm.eg.db”)
biocLite(“GOstats”)
biocLite(“KEGG.db”)
biocLite(“pathview”)
biocLite(“annotate”)
biocLite(“AnnotationDbi”)
install.packages(“gtools”)
install.packages(“fmsb”)
install.packages(“HybridMTest”)
e. Cytoscape.
Install from the following link version 3.6.1:
f. Regulatory Genomics ToolBoox (RGT) (not in Windows)
Install the software from the following site
http://www.regulatory-genomics.org/rgt/download-installation/
f. PyDNase (not in Windows)
https://pythonhosted.org/pyDNase/installation.html
g. javaTreeview
For the Visualization of Heatmaps.
http://jtreeview.sourceforge.net/
2. DOWNLOAD MATERIAL: DATA.
There will be internet connection during the course, but to avoid checking the limits of the bandwidth, we ask you all to download the necessary materials before the course.
For most of the material, we are using Dropbox as the sharing platform. Please remember that the link provides the option to download the material EVEN if you are not a Dropbox user or do not have enough space to add it to your Dropbox.
Available lectures to download are being added regularly at the following link: shared lectures.
0. STATegra DataSet:
The following data-set will be used in different sessions and can be used in the working projects.
The entire material can be downloaded from this link.
a. RNA-seq Material:
All session: Download from the dropbox link.
b. ATAC-seq Material:
ATAC-seq session: download from the dropbox link.
Integration session (1): download the material from the dropbox link.
Code for the integration session (1): download the file from dropbox link.
c. DNA Methylation Material:
DNA Methylation and integration session: download from the dropbox link.
d. Network Analysis:
Network Analysis session: download from the dropbox link.
e. Meta-Analysis and NPC:
Meta-analysis and NPC session: download from the dropbox link.
f. OmicsPCA:
OmicsPCA session: download from the dropbox link.
g. single-cell RNA-seq:
single-cell RNA-seq session:
UPDATED download the data and code from the Dropbox link.