Useful Resources

Here is a (non-exhaustive) list of resources that are useful for metabolomics research and general biomedical research.

RStudio

RStudio is a software that makes it easier to learn R. To download, go to:

Home

 

A quick introduction to R/RStudio can be found here:

http://ncss-tech.github.io/stats_for_soil_survey/chapters/1_introduction/1_introduction.html

 

And here is a much more thorough introduction to R:

https://cran.r-project.org/doc/manuals/r-release/R-intro.pdf

 

R/Rstudio very widely used in the metabolomics community, and in the general biomedical research community.  Most questions can thus be answered with google!  (e.g. you can paste your error message and follow them by “R” as a good way to start searching).

 

R packages related to metabolomics

 

R BioConductor contains widely used software for the preprocessing of metabolomics data (from raw data files to statistical analysis).  Here are some widely used software:

XCMS: https://bioconductor.org/packages/release/bioc/html/xcms.html

CAMERA: https://bioconductor.org/packages/release/bioc/html/CAMERA.html

MAIT: https://bioconductor.org/packages/release/bioc/html/MAIT.html

 

This list is not exhaustive and many tools are coming out rather frequently.

 

Other metabolomics software (that do not require knowledge of R)

MetaboAnalyst: https://www.metaboanalyst.ca/

Metabox: https://www.metaboanalyst.ca/

MS-Dial: http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/

MzMine: http://mzmine.github.io/

LipidMatch: http://secim.ufl.edu/secim-tools/lipidmatch/

 

 

General Metabolomics resources

Metabolomics Workbench: https://metabolomicsworkbench.org/

MANA: https://metabolomicsna.org/

Metabolomics Society: http://metabolomicssociety.org/

Fiehn Lab: http://fiehnlab.ucdavis.edu/