Material

All materials for the GTIPI 2022 Summer School are available at this GitHub repository - https://github.com/imbeimainz/GTIPI2022_materials.
Updates to this repository might be expected while the Summer School is still running.

Software requirements

Participants are required to bring their own laptop, with the most recent release versions of R and Bioconductor installed: R-4.2.0 and Bioconductor 3.15.
An IDE like RStudio is not mandatory, but very recommended.

For the R/Bioc & transcriptome analysis sessions (bulk and single cell), you will need some CRAN/Bioconductor packages - simply run this chunk in R/RStudio to install the ones required.

install.packages("BiocManager")
BiocManager::install()
BiocManager::install(
  c("knitr",
    "rmarkdown",
    "MASS",
    "ggplot2",
    "gapminder",
    "ggthemes",
    "tidyverse",
    "DESeq2",
    "tximeta",
    "org.Hs.eg.db",
    "edgeR",
    "ExploreModelMatrix",
    "pcaExplorer",
    "macrophage",
    "apeglm",
    "pheatmap",
    "iSEE",
    "iSEEu",
    "GeneTonic",
    "topGO",
    "clusterProfiler",
    "SingleCellExperiment",
    "TENxPBMCData",
    "scater",
    "scran",
    "dplyr",
    "celldex",
    "SingleR")
)

If this returns no errors, you should be all set.

You can test whether you can load the packages by running the lines of code included in this collapsible element (click to display)

library("knitr")
library("rmarkdown")
library("MASS")
library("ggplot2")
library("gapminder")
library("ggthemes")
library("tidyverse")
library("DESeq2")
library("tximeta")
library("org.Hs.eg.db")
library("edgeR")
library("ExploreModelMatrix")
library("pcaExplorer")
library("macrophage")
library("apeglm")
library("pheatmap")
library("iSEE")
library("iSEEu")
library("GeneTonic")
library("topGO")
library("clusterProfiler")
library("SingleCellExperiment")
library("TENxPBMCData")
library("scater")
library("scran")
library("dplyr")
library("celldex")
library("SingleR")

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Please try to set up your computer beforehand! While internet connection at the Summer School venue is available and we have a troubleshooting session on the day of arrival, it might be beneficial to have your system all set!