Informatics and Statistics for Metabolomics 2017 PreWork

1) A robust text editor.

• For Windows/PC - notepad++
• For Linux - gEdit
• For Mac – TextWrangler

2) A file decompression tool.

• For Windows/PC – 7zip.
• For Linux – gzip.
• For Mac – already there.

3) A robust internet browser such as Firefox or Safari (Internet Explorer and Chrome are not recommended because of Java issues).

4) Proteowizard MS convert.

5) Latest version of R.

6) XCMS on R, with all relevant packages as indicated here.
The R folder needs to allow writing of new libraries (override the windows default read-only), or download all the packages and transfer to another folder. check on R that the command line library(xcms) does not return an error (minor R version warning is okay).

7) A PDF viewer (Adobe Acrobat or equivalent).

Do these tutorials before the workshop

1) R Preparation tutorials: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before.

• The CBW R tutorial
• Quick and Dirty Guide to R
• The R Tutorial up to and including 5. Basic Plots
• The R command cheat sheet

Before coming to the workshop, read these:

• XCMS Online: a web-based platform to process untargeted metabolic data
• Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics
• HMDB 3.0–The Human Metabolome Database in 2013
• Introduction to Cheminformatics