Parameter file format in search gui

This is an issue regarding the parameter file format of the search gui software.
They are using a binary format to store the software configuration. I think it is a no go, so I did open up an issue on github, which was immediately closed.

https://github.com/compomics/searchgui/issues/60

8/10/2015 Update - it's open again....

Java Mass Spectrometry Resources for developers

Pride resources

https://github.com/PRIDE-Utilities/jmzReader

https://github.com/PRIDE-Utilities

http://www.mcponline.org/content/early/2015/11/06/mcp.O115.050229.abstract
https://github.com/PRIDE-Toolsuite
https://github.com/PRIDE-Toolsuite/pride-inspector/wiki

Compomics

https://github.com/compomics


   - https://github.com/compomics/peptide-shaker
   - https://github.com/compomics/searchgui

R classes with references resources

https://stat.ethz.ch/R-manual/R-devel/library/methods/html/refClass.html
http://adv-r.had.co.nz/OO-essentials.html
https://www.bioconductor.org/help/course-materials/2010/HeidelbergNovember2010/ReferenceClasses-Morgan.pdf

or type in R
?ReferenceClasses

Building Crux

Quite straightforward. Otherwise well documented here:
http://cruxtoolkit.sourceforge.net/install-tutorial.html

You will need wget with ssl and https. I got mine from :
https://eternallybored.org/misc/wget/


Running comet with crux?

Beware! crux comet and comet have different interfaces.

Comet - you can download from here:
http://comet-ms.sourceforge.net/

R Package Quantable

New package quantable on CRAN:

Methods which streamline the descriptive analysis of quantitative matrices.

https://cran.r-project.org/web/packages/quantable/index.html

Has some routines to simplify various plots (i.e. qqplot) for multivariate data. 

Also a nice volcano.

Most up to date version can be found here:
https://github.com/protViz/quantable