msGUI is a simple graphical user interface
to visualise and browse raw mass spectrometry data. It supporst data in
mzML via the
mzR infrastrucutre. It allows users to navigate MS1 and/or higher
level spectra as well as displaying (extracted) ion chromatograms.
RforProteomics illustrates the usage of several R/Bioconductor packages to analyse proteomics data. It provides all the code to reproduce the examples and figures of the Using R and Bioconductor for proteomics data analysis manuscript (submitted). The package is available from the Bioconductor project.
This Bioconductor package
which includes many more features) aims at providing a
reproducible research framework to the proteomics
community. It should allow researcher to easily mine
MS(MS) data, its statistical properties and visually display
these. Some underlying structures and use cases are presented
in these poster
(BSPR/EBI conference, July 2010)
Developer Meeting, November 2010).
MSnbase includes a demo vignette that illustrates
it's usage with dummy data included with the package. The
vignette is a good starting point to learn how to
MSnbase and can be accessed
is also a document that describes the underlying classes. See
the package documentation
?MSnbase and references
therein for more details.
synapter is a Bioconductor package to analyse MSE data. It allows to optimise identification and quantitation accuracy by tranfering identifications between multiple runs. An example html report is avaiable here. Several experimental designs, combining runs with or without ion mobilit separation and a complete workflow up to statistical analysis of a complete dataset are described in the vignette.
a Bioconductor package
that provides a unified API to the common file formats and
parsers available for mass spectrometry data. It comes with
a wrapper for
the ISB random
acces parser for
mzML files. The package contains the
original code written by the ISB, and a subset of
reading code has previously been used
is a joint effort
Neumann (IBP Halle) and Laurent Gatto (University of
a Bioconductor package
developed by Thomas Dybdal Pedersen and Vladislav A Petyuk
with support from Laurent Gatto that
mzIdentML files using
XML package. It supports versions 1.0 and
1.1 of the
RpepXML is an R package that allows to import
and manipulate generic MSMS identification data saved
for an browsable scheme). It is hosted
by R-Forge. Installation
and getting started information can be found on
package for the analysis and interpretation of
quantitative organelle MS data from a typical gradient
et al., Proteomics 2010) using the methods described in
the literature (protein correlation profiling, partial least
square discriminant analysis, support vector machines) as
well as novel approaches to asses sub-cellular
localisation. It relies on
structures to store quantitative proteomics data and the
associated meta data. Published data sets are available
experiment package. An interactive visualisation graphical
interface is currently under development.
sequences is a R package used in the frame of the Advanced R programming and development course. It implements generic sequences as a top virtual class and specific biological (DNA and RNA) sequences.
Cambridge R user group
CambR As R enthusiasts, we are eager to bring useRs of Cambridge and surroundings together to share their experiences using R. We are aiming at organising meetings in Cambridge, including talks, mini workshops, data analysis sessions,... with an emphasis on interaction among participants. We have set up a CambR google group to discuss any matter related to the CambR group and meetings or any other aspect related to R that you may want to share. Please feel free to register or get in contact with one of the organisers.
yaqcaffy is a Bioconductor package for the quality analysis of Affymetrix Expression GeneChips. The library basically does 2 things: (1) quality control analyses and (2) comparison of in-house MAQC reference RNAs with (a subset) of the MAQC reference datasets (depends on the MAQCsubsetAFX package). See the vignette for more details. This package has been written and tested in the frame of my bioinformatician position at DNAVision.
MAQCsubsetILM are Bioconductor data packages. They include one MAQC data file (raw
CEL files in case of
MAQCsubsetAFX) out of 5 replicates par test site. These two packages have been written and tested in the frame of my bioinformatician position at DNAVision.