# 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'))