R and Bioconductor for proteomics at the Sainsbury Laboratory

This repository will host the OpenPlant funded R/Bioconductor for proteomics material. The funding was awarded to Jan Sklenar (TSL, Norwich), Laurent Gatto (UCam), Marielle Vigouroux (JIC), Govind Chandra (JIC) to introduce and implement the utilisation of various R for proteomics tools in the Sainsbury Laboratory and more generally on the Norwich campus.

The project will run 6 sessions/days over 6 months with the aim to

• Identify needs and opportunities
• Train invdividuals
• Dedicated development and integration with existing tools

Session 1: Setting the stage (15 Jan 2018)

• Introductory talk: R and Bioconductor for proteomics

During this session, we discussed the concrete needs and opportunities that would be tackled as part of this project, and set a schedule for the sessions until June.

Session 2: Hands-on introduction to R and Bioconductor for proteomcs (2 Feb 2018)

Software requirements: R and RStudio

Download and install R and RStudio. In case you already have R installed, make you have R 3.4.3. To check the version:

> version
               _                                          
platform       x86_64-pc-linux-gnu                        
arch           x86_64                                     
os             linux-gnu                                  
system         x86_64, linux-gnu                          
status         Patched                                    
major          3                                          
minor          4.3                                        
year           2017                                       
month          12                                         
day            12                                         
svn rev        73903                                      
language       R                                          
version.string R version 3.4.3 Patched (2017-12-12 r73903)
nickname       Kite-Eating Tree

Once the software are installed, open RStudio and install Bioconcuctor packages:

source("http://www.bioconductor.org/biocLite.R")
biocLite(c("MSnbase", "msmsTests", "rpx", "pRoloc", "pRolocdata", "msdata"))

To test the installation, load MSnbase:

library("MSnbase")

Programme

• Introduction to R and RStudio and Bioconductor
• R documentation and vignettes
• Variables, vectors and dataframes
• Manipulating data
• Plotting
• Saving and loading data (binary and csv)
• Installing packages