R Graphical Manual

Last data update: 2014.03.03

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xcms : LC/MS and GC/MS Data Analysis

Package: xcms
Version: 1.48.0
Date: 2016-05-02
Title: LC/MS and GC/MS Data Analysis
Author: Colin A. Smith <csmith@scripps.edu>,
Ralf Tautenhahn <rtautenh@gmail.com>,
Steffen Neumann <sneumann@ipb-halle.de>,
Paul Benton <hpbenton@scripps.edu>,
Christopher Conley <cjconley@ucdavis.edu>,
Johannes Rainer <Johannes.Rainer@eurac.edu>
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
Depends: R (>= 2.14.0), methods, mzR (>= 1.1.6), BiocGenerics,
ProtGenerics, Biobase
Imports: lattice, RColorBrewer
Suggests: faahKO, msdata, ncdf4, multtest, rgl, MassSpecWavelet (>=
1.5.2), RANN, RUnit, parallel
Enhances: Rgraphviz, Rmpi, XML
Description: Framework for processing and visualization of
chromatographically separated and single-spectra mass spectral data. Imports from
AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for
high-throughput, untargeted analyte profiling.
License: GPL (>= 2) + file LICENSE
URL: http://metlin.scripps.edu/download/
https://github.com/sneumann/xcms
BugReports: https://github.com/sneumann/xcms/issues/new
biocViews: MassSpectrometry, Metabolomics
NeedsCompilation: yes
Packaged: 2016-05-04 02:46:06 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: MassSpectrometry, Metabolomics
● 7 images, 97 functions, 0 datasets
● Reverse Depends: 7

MSGFgui : A shiny GUI for MSGFplus

Package: MSGFgui
Type: Package
Title: A shiny GUI for MSGFplus
Version: 1.6.2
Date: 2015-02-03
Author: Thomas Lin Pedersen
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Description: This package makes it possible to perform analyses using
the MSGFplus package in a GUI environment. Furthermore it
enables the user to investigate the results using interactive
plots, summary statistics and filtering. Lastly it exposes the
current results to another R session so the user can seamlessly
integrate the gui into other workflows.
License: GPL (>= 2)
LazyLoad: yes
biocViews: MassSpectrometry, Proteomics, GUI, Visualization
VignetteBuilder: knitr
Depends: mzR, xlsx
Imports: shiny, mzID (>= 1.2), MSGFplus, shinyFiles (>= 0.4.0), tools
Suggests: knitr, testthat
Collate: 'MSGFgui-package.R' 'server_functions.R' 'server.R'
'MSGFgui.R'
NeedsCompilation: no
Packaged: 2016-05-16 04:55:35 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: GUI, MassSpectrometry, Proteomics, Visualization
● 0 images, 3 functions, 0 datasets
● Reverse Depends: 0

MSnbase : Base Functions and Classes for MS-based Proteomics

Package: MSnbase
Title: Base Functions and Classes for MS-based Proteomics
Version: 1.20.7
Description: Basic plotting, data manipulation and processing
of MS-based Proteomics data.
Authors@R: c(person(given = "Laurent", family = "Gatto",
email = "lg390@cam.ac.uk",
role = c("aut","cre")),
person(given = "Guangchuang", family ="Yu",
email = "guangchuangyu@gmail.com",
role = "ctb"),
person(given = "Samuel", family ="Wieczorek",
email = "samuel.wieczorek@cea.fr",
role = "ctb"),
person(given = "Vasile-Cosmin", family ="Lazar",
email = "v.cosmin.lazar@googlemail.com",
role = "ctb"),
person(given = "Vladislav", family ="Petyuk",
email = "petyuk@gmail.com",
role = "ctb"),
person(given = "Thomas", family ="Naake",
email = "tn299@cam.ac.uk",
role = "ctb"),
person(given = "Richie", family ="Cotton",
email = "richierocks@gmail.com",
role = "ctb"),
person(given = "Martina", family ="Fischer",
email = "FischerM@rki.de",
role = "ctb"),
person(given = "Gibb", family ="Sebastian",
email = "mail@sebastiangibb.de",
role = "ctb"))
Author: Laurent Gatto <lg390@cam.ac.uk> with contributions from
Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar,
Vladislav Petyuk, Thomas Naake, Richie Cotton, Martina Fisher
and Sebastian Gibb.
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
Depends: R (>= 3.1), methods, BiocGenerics (>= 0.7.1), Biobase (>=
2.15.2), mzR, BiocParallel, ProtGenerics (>= 1.3.1)
Imports: plyr, IRanges, preprocessCore, vsn, grid, reshape2, stats4,
affy, impute, pcaMethods, mzID (>= 1.5.2), MALDIquant (>=
1.12), digest, lattice, ggplot2, S4Vectors, Rcpp
Suggests: testthat, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc,
pRolocdata (>= 1.7.1), msdata, roxygen2, rgl, BiocStyle,
imputeLCMD, norm, gplots, shiny
LinkingTo: Rcpp
License: Artistic-2.0
LazyData: yes
VignetteBuilder: knitr
BugReports: https://github.com/lgatto/MSnbase/issues
URL: https://github.com/lgatto/MSnbase
biocViews: Infrastructure, Proteomics, MassSpectrometry,
QualityControl, DataImport
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-26 02:50:18 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl
● 41 images, 70 functions, 3 datasets
● Reverse Depends: 9