--- a
+++ b/set_up.R
@@ -0,0 +1,36 @@
+# This file contains intallation instructions for packages required to run Find_molecular_subtypes_TCGA.ipynb. 
+
+# We will need:
+#  - tidyverse, reticulate, tsne, factoextra and plyr for data exploration and wrangling,
+#  - ComplexHeatmap, ggalluvial, ggpubr, survival, survminer, GGally for plotting,
+#  - FactoMineR, NMF, PINSPlus and iClusterPlus for data integration.
+
+# Hint: Try attaching required packages before the installation to check if they are not already installed on your machine / in your environment.
+library(plyr)
+library(tidyverse)
+library(ComplexHeatmap)
+library(ggalluvial)
+library(ggpubr)
+library(FactoMineR)
+library(PINSPlus)
+library(iClusterPlus)
+library(RColorBrewer)
+library(tsne)
+library(reticulate)
+library(survival)
+library(survminer)
+library(factoextra)
+library(GGally)
+library(enrichR)
+
+
+# Install Bioconductor packages
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("ComplexHeatmap")
+BiocManager::install("iClusterPlus")
+
+# Install other required packages
+install.packages(c('plyr', 'tidyverse', 'ggalluvial', 'ggpubr', 'FactoMineR', 'PINSPlus', 'RColorBrewer', 'tsne', 
+                   'reticulate', 'survival', 'survminer', 'factoextra', 'GGally', 'enrichR'))