InstallationInstructions.txt

##For the lecuters:
#Please install ZOOM: https://zoom.us/download
#Please join the slack channel: https://join.slack.com/t/singlecellcoursehd/shared_invite/zt-pn61ha5c-GG0IMBiOWlo5mH4ZJjsCWA
#Optionally: install the slack app: https://slack.com/intl/en-de/

##For the tutorials (day1-day2): 

##Step 0.
#Install Anaconda or miniconda
#(information see: https://docs.anaconda.com/anaconda/install/)

##Step 1.
#After installation you will automatically load the base enviroment.
#These instructions will install software in the "base" enviroment but you can also make a specific enviroment for the course.
# To do so use: "conda create --name myenv" & "conda activate myenv" (myenv can be replaced with a name of choice)
# If you create an enviroment please specify Python 3.7

##Step 2.
#Install R 4 (conda forge)
conda install -c conda-forge r-base=4

##Step 3.
##install other dependancies within R!
#Start R
R
(within R)
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.11")

BiocManager::install("scran")
BiocManager::install("scater")
BiocManager::install("umap")
BiocManager::install("Rtsne")
BiocManager::install("dplyr")
BiocManager::install("ggplot2")
BiocManager::install("data.table")
BiocManager::install("SingleCellExperiment")
BiocManager::install("MOFA")
devtools::install_github("bioFAM/MOFA2", build_opts = c("--no-resave-data --no-build-vignettes"))
install.packages('Seurat')

##Step 4.
#Please try and load the packages in R. 
#Specifically for "Seurat" make sure you load the library at least once "library("Seurat")" and install the remaining dependancies via miniconda.

##Step 5.
# To install the dependencies for the day3 please follow the instructions here: https://github.com/PMBio/SingleCellCourse/blob/master/day3/installation.md