R Course for the Life Science Community

This course presents a comprehensive overview of the statistical programming language R using the LRZ hardware capabilities. The course combines lectures with hands-on exercises in which the participants learn to apply R to real biomedical datasets.

Within the last 10 years, more and more researchers using R have run their projects at the Leibniz Supercomputing center (LRZ). In the course, we will present the different approaches that have been applied in the last years in order to port R-scripts, which have originally been run on commodity hardware, to the various HPC systems at LRZ. 

We will illustrate the HPC approaches using a wide variety of R packages including multicore, snow, rredis, snowfall,the various 'do-variants' (doMC, doRedis, doSNOW), BatchExperiments and the MPI based packages RMPI and pbdMPI.

A special focus is put on the Bioconductor packages for Next Generation Sequencing.

Agenda:

1. Introduction to LRZ HPC services

2. R & Rstudio at LRZ

3. Introduction to the R Language

4. Bioconductor

   1. Overview
   2. NGS

5. parallel programming using R at LRZ

   1. library(parallel)
   2. library(doMC), library(doMPI), library(doRedis)
   3. snow and snowfall, doSNOW at LRZ