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DESCRIPTION
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DESCRIPTION
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Package: MSnbase
Title: Base Functions and Classes for Mass Spectrometry and Proteomics
Version: 2.31.2
Description: MSnbase provides infrastructure for manipulation,
processing and visualisation of mass spectrometry and
proteomics data, ranging from raw to quantitative and
annotated data.
Authors@R: c(person(given = "Laurent", family = "Gatto",
email = "laurent.gatto@uclouvain.be",
comment = c(ORCID = "0000-0002-1520-2268"),
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 = "Steffen", family = "Neumann",
email = "sneumann@ipb-halle.de",
role = "ctb"),
person(given = "Arne", family = "Smits",
email = "arne.smits@embl.de",
role = "ctb"),
person(given = "Martina", family = "Fischer",
email = "FischerM@rki.de",
role = "ctb"),
person(given = "Adriaan", family = "Sticker",
email = "adriaan.sticker@ugent.be",
role = "ctb"),
person(given = "Ludger", family = "Goeminne",
email = " ludger.goeminne@vib-ugent.be",
role = "ctb"),
person(given = "Lieven", family = "Clement",
email = "Lieven.Clement@ugent.be",
role = "ctb"),
person(given = "Sigurdur", family = "Smarason",
email = " Sigurdur.Smarason@eurac.edu",
role = "ctb"),
person(given = "Miguel", family = "Cosenza-Contreras",
email = "migueljcc5@gmail.com",
role = "ctb"),
person(given = "Pascal", family = "Maas",
email = "p.maas@lacdr.leidenuniv.nl",
comment = c(ORCID = "0000-0001-9379-6041"),
role = "ctb"),
person(given = "Johannes", family = "Rainer",
email = "Johannes.Rainer@eurac.edu",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-6977-7147")),
person(given = "Sebastian", family = "Gibb",
email = "mail@sebastiangibb.de",
role = c("aut", "cre"),
comment=c(ORCID="0000-0001-7406-4443")))
Author: Laurent Gatto, Johannes Rainer and Sebastian Gibb with
contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin
Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits,
Martina Fisher, Ludger Goeminne, Adriaan Sticker, Lieven
Clement and Pascal Maas.
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
Depends:
R (>= 3.5),
methods,
BiocGenerics (>= 0.7.1),
Biobase (>= 2.15.2),
mzR (>= 2.29.3),
S4Vectors,
ProtGenerics (>= 1.29.1)
Imports:
MsCoreUtils,
PSMatch,
BiocParallel,
IRanges (>= 2.13.28),
plyr,
vsn,
grid,
stats4,
affy,
impute,
pcaMethods,
MALDIquant (>= 1.16),
mzID (>= 1.5.2),
digest,
lattice,
ggplot2,
scales,
MASS,
Rcpp
Suggests:
testthat,
pryr,
gridExtra,
microbenchmark,
zoo,
knitr (>= 1.1.0),
rols,
Rdisop,
pRoloc,
pRolocdata (>= 1.43.3),
magick,
msdata (>= 0.19.3),
roxygen2,
rgl,
rpx,
AnnotationHub,
BiocStyle (>= 2.5.19),
rmarkdown,
imputeLCMD,
norm,
gplots,
XML,
shiny,
magrittr,
SummarizedExperiment
LinkingTo: Rcpp
License: Artistic-2.0
LazyData: yes
VignetteBuilder: knitr
Encoding: UTF-8
BugReports: https://github.com/lgatto/MSnbase/issues
URL: https://lgatto.github.io/MSnbase
biocViews: ImmunoOncology, Infrastructure, Proteomics, MassSpectrometry,
QualityControl, DataImport
Roxygen: list(markdown=TRUE)
RoxygenNote: 7.3.1
Collate:
'AllClassUnions.R'
'AllGenerics.R'
'DataClasses.R'
'MzTab.R'
'NAnnotatedDataFrame.R'
'NTR.R'
'RcppExports.R'
'TMT10.R'
'TMT11.R'
'TMT16.R'
'TMT6.R'
'TMT7.R'
'averageMSnSet.R'
'cache.R'
'coerce.R'
'combineFeatures.R'
'compfnames.R'
'environment.R'
'fData-utils.R'
'fdata-selection.R'
'foi.R'
'functions-Chromatogram.R'
'functions-MChromatograms.R'
'functions-MIAPE.R'
'functions-MSnExp.R'
'functions-MSnProcess.R'
'functions-MSnSet.R'
'functions-MSpectra.R'
'functions-OnDiskMSnExp.R'
'functions-ReporterIons.R'
'functions-Spectrum.R'
'functions-Spectrum1.R'
'functions-Spectrum2.R'
'functions-addIdentificationData.R'
'functions-mzR.R'
'functions-plotting.R'
'hmap.R'
'iPQF.R'
'iTRAQ4.R'
'iTRAQ5.R'
'iTRAQ8.R'
'iTRAQ9.R'
'imputation.R'
'map.R'
'matching.R'
'methods-Chromatogram.R'
'methods-MChromatograms.R'
'methods-MIAPE.R'
'methods-MSnExp.R'
'methods-MSnProcess.R'
'methods-MSnSet.R'
'methods-MSnSetList.R'
'methods-MSpectra.R'
'methods-OnDiskMSnExp.R'
'methods-ReporterIons.R'
'methods-Spectrum.R'
'methods-Spectrum1.R'
'methods-Spectrum2.R'
'methods-all.equal.R'
'methods-filters.R'
'methods-fragments.R'
'methods-mzR.R'
'methods-other.R'
'methods-pSet.R'
'methods-updateObjectTo.R'
'methods-write.R'
'missing-data.R'
'nadata.R'
'nav.R'
'options.R'
'plotting-MSnExp.R'
'plotting-MSnSet.R'
'plotting-Spectrum.R'
'plotting-Spectrum1.R'
'plotting-Spectrum2.R'
'plotting-dataframe.R'
'quantitation-MS2-isobaric.R'
'quantitation-MS2-labelfree.R'
'readChromData.R'
'readMSData.R'
'readMSData2.R'
'readMSnSet.R'
'readMzXMLData.R'
'readWriteMgfData.R'
'readWriteMzTab.R'
'utils.R'
'writeMSData.R'
'zzz.R'