MIP Computational Proteomics (CPX) Resource
CPX Software
- NITPICK R-packages
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These are the R packages for our BMC Bioinformatics publication entitled
NITPICK: Peak Identification for Mass Spectrometry Data
The nitpick and iwrlars packages are 100% R code and will run on any operating system. However, amsmercury relies on libmercury++ (see below) and needs to be compiled. All packages have been built and tested under Linux; we use them in a Unix cluster environment and are thus unable to provide Microsoft Windows runtimes for amsmercury.
The NITPICK C++ library is under development and will be publicly available in autumn/winter 2008.
IMPORTANT NOTICE: Due to a source code archiving issue, NITPICK downloads prior to Sep 17, 2008, 05:15pm CET lack the amsaveragine R package. An updated source archive is available. We are sorry for the inconvenience.
- libmercury++
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libmercury++ is an ANSI-C++ library re-implementation of Rockwood's Mercury7
algorithm, in parts based on the emass code of Perttu Haimi. Documentationwise, the
source documentation and the demo.cpp file should be sufficient.
Elements are still limited to H, C, N, O, S. This is no limitation to the program, but merely a question of entering all isotope data into the static tables. libmercury++ is the main building block of the amsmercury R package (see above).
libmercury++ is licensed under LGPL.
Please direct requests to Marc. - amsrpm
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amsrpm is an R-package for TIC and LC/MS peak alignment. It is based on functional data analysis
methods, as described in Ramsay and Silverman, 1997.
Code and the related publication are available as part of a Special Volume an Spectroscopy and Chemometrics in R ofthe Journal of Statistical Software.
In the meantime we have developed much more sophisticated algorithms for the alignment/registration of LC/MS datasets which are pending publication.
Contact Marc for further information.
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Last update: 17.09.2008, 17:17 |
Webmaster: Ole Hansen
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