UiB Blogg            

Software installation instructions for ‘Large genetic studies in biobanks: from registries screening, to interpretation of GWAS and beyond’


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)
here
 
Haploview (please also download the two example files)
here
 
GSEA
here
 
MAGMA
here
 
gcta
here
 
R
here
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
here
 
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.