In preparation for the course, it is necessary to install some software and R-packages in advance. Installation should usually be unproblematic, but it’s good to get it done and run some tests before the course. Please follow the links for download:
PLINK 2 (examples are prepared in 1.9)
Haploview (please also download the two example files)
GSEA
MAGMA
gcta
R
here
Libraries:
Libraries:
- from CRAN; ggplot2, lmtest, qqman, rstan, scatterplot3d: install by running > install.packages(“package_name”)
- LDsnpR; from source install.packages(path_to_file, repos = NULL, type = “source”)
Data:
- Genotype file example.bed/.bim/.fam
- Hdf5file
- LDsnpR package
- R scripts
RStudio
Windows users should also install some environment to run bash scripts.
There are plenty of ways to do this. One easy way is to install git for Windows; from here. It comes with bash emulator. People using Windows 10 can install Windows Subsystem for Linux. Other alternatives are Cygwin and MinGW.