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Precourse preparations

R and RStudio

Previous knowledge / Competencies

We expect participants to have previous knowledge in:

  • R beginner level (Rstudio, install a library, data frame manipulation, import data from csv file). An introduction to R is available here.

Technical

This course will be streamed, you are thus required to have your own computer with an internet connection, and with latest the version of R and the free version of RStudio installed. Admin rights may be needed to install the necessary packages.

The packages we will need are hosted on CRAN, Bioconductor and Github. You can install the necessary packages using:

#################################
# Non-CRAN package installation #
#################################

install.packages("devtools")
install.packages("BiocManager")


###############
# R markdown  #
###############

install.packages("knitr")
install.packages("rmarkdown")
install.packages("pander")


#####################
# Excel files       #
#####################

install.packages("readxl")
install.packages("xlsx")
install.packages("WriteXLS")


#################
# Visualization #
#################

install.packages("ggplot2")
BiocManager::install("ggcyto")
install.packages("manipulate")
install.packages("ggrepel")
install.packages("ggpubr")
install.packages("RColorBrewer")
install.packages("gridExtra")
install.packages("cowplot")
install.packages("ggsignif")
BiocManager::install("plotly")
install.packages("ggridges")
install.packages("scales")
BiocManager::install("ComplexHeatmap")
install.packages("circlize")
install.packages("cowplot")

#################
# Data handling #
#################

install.packages("reshape2")
install.packages("matrixStats")
install.packages("tidyverse")
install.packages("dplyr")
install.packages("tibble")


###############################################
# Statistical functions                       #
###############################################

install.packages("lme4")
install.packages("multcomp")
install.packages("rstatix")
install.packages("DescTools")
install.packages("statmod")
BiocManager::install("edgeR")
install.packages("MASS")
BiocManager::install("diffcyt")
install.packages('sfsmisc')
install.packages("rms")


#########################################
# Libraries for flow cytometry analysis #
#########################################

BiocManager::install("flowCore")
BiocManager::install("flowWorkspace")
BiocManager::install("flowWorkspaceData")
BiocManager::install("flowDensity")
BiocManager::install("MetaCyto")
BiocManager::install("scDataviz")
BiocManager::install("flowViz")
BiocManager::install("flowVS")
BiocManager::install("flowAI")
BiocManager::install("PeacoQC")
BiocManager::install("flowClean")
BiocManager::install("CATALYST")
devtools::install_github('saeyslab/CytoNorm')
BiocManager::install("SingleCellExperiment")
install.packages("uwot")
BiocManager::install("FlowSOM")
BiocManager::install("ConsensusClusterPlus")
install.packages("Rtsne")
BiocManager::install("scater")
devtools::install_github("RGLab/scamp")
devtools::install_github("RGLab/FAUST")
BiocManager::install("flowStats")
BiocManager::install("destiny")
BiocManager::install("slingshot")
devtools::install_github("JinmiaoChenLab/cytofkit2", dependencies=TRUE)


############################
# Survival analysis        #
############################

install.packages("survival")
install.packages("survminer")

############################
# Gating                   #
############################

BiocManager::install("flowClust")
BiocManager::install("CytoML")
BiocManager::install("openCyto")

After installation, packages can be loaded using:

#################################
# Non-CRAN package installation #
#################################

# install packages
library(devtools) # install.packages("devtools")
library(BiocManager) # install.packages("BiocManager")


###############
# R markdown  #
###############

library(knitr) # install.packages("knitr")
library(rmarkdown) # install.packages("rmarkdown")
library(pander) # install.packages("pander")


#####################
# Excel files       #
#####################

library(readxl) # install.packages("readxl")
library(xlsx) # install.packages("xlsx")
library(WriteXLS) # install.packages("WriteXLS")


#################
# Visualization #
#################

library(ggplot2) # install.packages("ggplot2")
library(ggcyto) # BiocManager::install("ggcyto")
library(manipulate) # install.packages("manipulate")
library(ggrepel) # install.packages("ggrepel")
library(ggpubr) # install.packages("ggpubr")
library(RColorBrewer) # install.packages("RColorBrewer")
library(gridExtra) # install.packages("gridExtra")
library(cowplot) # install.packages("cowplot")
library(ggsignif) # install.packages("ggsignif")
library(plotly) # BiocManager::install("plotly")
library(ggridges) # install.packages("ggridges")
library(scales) # install.packages("scales")
library(ComplexHeatmap) # BiocManager::install("ComplexHeatmap")
library(circlize) # install.packages("circlize")
library(cowplot) # install.packages("cowplot")


#################
# Data handling #
#################

library(reshape2) # install.packages("reshape2")
library(matrixStats) # install.packages("matrixStats")
library(tidyverse) # install.packages("tidyverse")
library(dplyr) # install.packages("dplyr")
library(tibble) # install.packages("tibble")


###############################################
# Statistical functions                       #
###############################################

library(lme4) # install.packages("lme4")
library(multcomp) # install.packages("multcomp")
library(rstatix) # install.packages("rstatix")
library(DescTools) # install.packages("DescTools")
library(statmod) # install.packages("statmod")
library(edgeR) # BiocManager::install("edgeR")
library(MASS) # install.packages("MASS")
library(diffcyt) # BiocManager::install("diffcyt")
library(sfsmisc) # install.packages('sfsmisc')
library(rms) # install.packages("rms")

#########################################
# Libraries for flow cytometry analysis #
#########################################

library(flowCore) # BiocManager::install("flowCore")
library(flowWorkspace) # BiocManager::install("flowWorkspace")
library(flowWorkspaceData) # BiocManager::install("flowWorkspaceData")
library(flowDensity) # BiocManager::install("flowDensity")
library(MetaCyto) # BiocManager::install("MetaCyto")
library(scDataviz) # BiocManager::install("scDataviz")
library(flowViz) # BiocManager::install("flowViz")
library(flowVS) # BiocManager::install("flowVS")
library(flowAI) # BiocManager::install("flowAI")
library(PeacoQC) # BiocManager::install("PeacoQC")
library("flowClean") # BiocManager::install("flowClean")
library(CATALYST) # BiocManager::install("CATALYST")
library(CytoNorm) # install_github('saeyslab/CytoNorm')
library(SingleCellExperiment) # BiocManager::install("SingleCellExperiment")
library(uwot)  # install.packages("uwot")
library(FlowSOM) # BiocManager::install("FlowSOM")
library(ConsensusClusterPlus) # BiocManager::install("ConsensusClusterPlus")
library(Rtsne) # install.packages("Rtsne")
library(scater) # BiocManager::install("scater")
library(scamp) # devtools::install_github("RGLab/scamp")
library(faust) # devtools::install_github("RGLab/FAUST")
library(flowStats) # BiocManager::install("flowStats")
library(destiny) # BiocManager::install("destiny")
library(slingshot) # BiocManager::install("slingshot")
library(cytofkit2) # devtools::install_github("JinmiaoChenLab/cytofkit2", dependencies=TRUE)


############################
# Survival analysis        #
############################

library(survival) # install.packages("survival")
library(survminer) # install.packages("survminer")

############################
# Gating                   #
############################

library(flowClust) # BiocManager::install("flowClust")
library(CytoML) # BiocManager::install("CytoML")
library(openCyto) # BiocManager::install("openCyto")