Package: synapter
Type: Package
Title: Label-free data analysis pipeline for optimal identification and
quantitation
Version: 1.14.2
Author: Laurent Gatto, Nick J. Bond and Pavel V. Shliaha
and Sebastian Gibb.
Maintainer: Laurent Gatto <lg390@cam.ac.uk> and
Sebastian Gibb <mail@sebastiangibb.de>
Depends: R (>= 2.15), methods, MSnbase
Imports: hwriter, RColorBrewer, lattice, qvalue, multtest, utils, Biobase, knitr, Biostrings, cleaver, BiocParallel
Suggests: synapterdata, xtable, tcltk, BiocStyle
Description: The synapter package provides functionality to reanalyse
label-free proteomics data acquired on a Synapt G2 mass
spectrometer. One or several runs, possibly processed with
additional ion mobility separation to increase identification
accuracy can be combined to other quantitation files to
maximise identification and quantitation accuracy.
License: GPL-2
URL: http://lgatto.github.com/synapter/
VignetteBuilder: knitr
biocViews: MassSpectrometry, Proteomics, GUI
NeedsCompilation: no
Packaged: 2016-05-16 03:30:37 UTC; biocbuild
Package: proteoQC
Type: Package
Title: An R package for proteomics data quality control
Version: 1.8.2
Author: Bo Wen <wenbo@genomics.cn>, Laurent Gatto <lg390@cam.ac.uk>
Maintainer: Bo Wen <wenbo@genomics.cn>
Description: This package creates a HTML format QC report for MS/MS-based
proteomics data. The report is intended to allow the user to quickly assess
the quality of proteomics data.
Depends: R (>= 3.0.0), XML, VennDiagram, MSnbase
Imports: rTANDEM, plyr, seqinr, Nozzle.R1, ggplot2, reshape2, parallel, Rcpp (>= 0.11.1)
LinkingTo: Rcpp
License: LGPL-2
Suggests: RforProteomics, knitr, BiocStyle, rpx, R.utils, RUnit, BiocGenerics
VignetteBuilder: knitr
biocViews: Proteomics, MassSpectrometry, QualityControl, Visualization,
ReportWriting
NeedsCompilation: yes
Packaged: 2016-05-16 04:34:10 UTC; biocbuild
Package: msmsEDA
Type: Package
Title: Exploratory Data Analysis of LC-MS/MS data by spectral counts
Version: 1.10.0
Date: 2014-01-19
Author: Josep Gregori, Alex Sanchez, and Josep Villanueva
Maintainer: Josep Gregori <josep.gregori@gmail.com>
Depends: R (>= 3.0.1), MSnbase
Imports: MASS, gplots, RColorBrewer
Description: Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.
License: GPL-2
Encoding: latin1
biocViews: Software, MassSpectrometry, Proteomics
NeedsCompilation: no
Packaged: 2016-05-04 05:01:37 UTC; biocbuild
Package: msmsTests
Type: Package
Title: LC-MS/MS Differential Expression Tests
Version: 1.10.0
Date: 2013-10-02
Author: Josep Gregori, Alex Sanchez, and Josep Villanueva
Maintainer: Josep Gregori i Font <josep.gregori@gmail.com>
Depends: R (>= 3.0.1), MSnbase, msmsEDA
Imports: edgeR, qvalue
Description: Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.
License: GPL-2
biocViews: Software, MassSpectrometry, Proteomics
NeedsCompilation: no
Packaged: 2016-05-04 05:02:35 UTC; biocbuild
Package: pRolocdata
Type: Package
Title: Data accompanying the pRoloc package
Version: 1.10.0
Author: Laurent Gatto and Lisa M. Breckels
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
Description: Mass-spectrometry based spatial proteomics data sets from
Dunkley et al. (2006), Foster et al. (2006), Tan et
al. (2009), Hall et al. (2009), Trotter et al. (2010),
Ferro et al. (2010), Nikolovski et al. (2012, 2014),
Breckels et al. (2013), Groen et al. (2014) and
Christoforou et al. (2015), and protein complex
separation data from Kristensen et al. (2012), Havugimana
et al. (2012), Kirkwood et al. (2013) Fabre et
al. (2015) and Mulvey et al. (2015).
Depends: R (>= 2.15), MSnbase
Imports: Biobase, utils
Suggests: pRoloc, testthat
License: GPL-2
BugReports: https://github.com/lgatto/pRolocdata/issues
URL: https://github.com/lgatto/pRolocdata
biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData,
Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data,
Mus_musculus_Data, StemCell
NeedsCompilation: no
Packaged: 2016-05-07 20:28:36 UTC; biocbuild
providing 
.