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Package: tofsims
Type: Package
Title: Import, process and analysis of Time-of-Flight Secondary Ion
Mass Spectrometry (ToF-SIMS) imaging data
Version: 1.0.2
Author: Lorenz Gerber, Viet Mai Hoang
Maintainer: Lorenz Gerber <genfys@gmail.com>
Depends: R (>= 3.3.0), methods , utils , ProtGenerics
Description: This packages offers a pipeline for import, processing and analysis of ToF-SIMS
2D image data. Import of Iontof and Ulvac-Phi raw or preprocessed data is
supported. For rawdata, mass calibration, peak picking and peak integration exist.
General funcionality includes data binning, scaling, image subsetting and
visualization. A range of multivariate tools common in the ToF-SIMS community are
implemented (PCA, MCR, MAF, MNF). An interface to the bioconductor image processing
package EBImage offers image segmentation functionality.
License: GPL-3
Imports: Rcpp (>= 0.11.2), ALS , ChemometricsWithR , signal , KernSmooth ,
graphics , grDevices , stats
Suggests: EBImage , knitr , rmarkdown , testthat , tofsimsData ,
BiocParallel , RColorBrewer
Enhances: parallel
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
biocViews: Infrastructure, DataImport, MassSpectrometry,
ImagingMassSpectrometry, Proteomics, Metabolomics
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-16 05:55:18 UTC; biocbuild
● Data Source:
BioConductor
● BiocViews: DataImport, ImagingMassSpectrometry, Infrastructure, MassSpectrometry, Metabolomics, Proteomics
●
33 images ,
114 functions ,
0 datasets
●
Reverse Depends: 0
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
Package: Cardinal
Type: Package
Title: A mass spectrometry imaging toolbox for statistical analysis
Version: 1.4.0
Date: 2015-1-12
Author: Kyle D. Bemis <kbemis@purdue.edu>
Maintainer: Kyle D. Bemis <kbemis@purdue.edu>
Description: Implements statistical & computational tools for analyzing
mass spectrometry imaging datasets, including methods for efficient
pre-processing, spatial segmentation, and classification.
License: Artistic-2.0
Depends: BiocGenerics , Biobase , graphics , methods , stats , ProtGenerics
Imports: grid , irlba , lattice , signal , sp , stats4 , utils
Suggests: BiocStyle , testthat
biocViews: Software, Infrastructure, Proteomics, Lipidomics,
Normalization, MassSpectrometry, ImagingMassSpectrometry,
Clustering, Classification
URL: http://www.cardinalmsi.org
NeedsCompilation: yes
Packaged: 2016-05-04 06:05:05 UTC; biocbuild
● Data Source:
BioConductor
● BiocViews: Classification, Clustering, ImagingMassSpectrometry, Infrastructure, Lipidomics, MassSpectrometry, Normalization, Proteomics, Software
●
25 images ,
45 functions ,
0 datasets
●
Reverse Depends: 1
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