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MALDIquant  

Quantitative Analysis of Mass Spectrometry Data
View on CRAN: Click here


Download and install MALDIquant package within the R console
Install from CRAN:
install.packages("MALDIquant")

Install from Github:
library("remotes")
install_github("cran/MALDIquant")

Install by package version:
library("remotes")
install_version("MALDIquant", "1.22.2")



Attach the package and use:
library("MALDIquant")
Maintained by
Sebastian Gibb
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2011-02-22
Latest Update: 2023-03-20
Description:
A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
How to cite:
Sebastian Gibb (2011). MALDIquant: Quantitative Analysis of Mass Spectrometry Data. R package version 1.22.2, https://cran.r-project.org/web/packages/MALDIquant
Previous versions and publish date:
0.1 (2011-02-22 19:22), 0.2 (2011-03-29 12:24), 0.3 (2011-05-29 09:54), 0.4 (2011-08-05 08:10), 0.5 (2012-01-18 18:14), 1.0 (2012-03-28 13:09), 1.1 (2012-05-06 17:24), 1.2 (2012-07-18 15:13), 1.3 (2012-09-16 19:53), 1.4 (2012-10-30 13:33), 1.5 (2012-12-07 10:13), 1.6 (2013-03-01 17:40), 1.7 (2013-05-23 19:38), 1.8 (2013-09-08 14:51), 1.9 (2014-01-14 16:43), 1.10 (2014-04-11 22:49), 1.11 (2014-08-11 21:39), 1.12 (2015-06-11 18:22), 1.13 (2015-09-16 12:47), 1.14 (2015-11-18 15:48), 1.15 (2016-06-25 19:46), 1.16.1 (2017-01-11 00:44), 1.16.2 (2017-04-04 17:45), 1.16.4 (2017-09-01 11:48), 1.16 (2016-12-14 00:57), 1.17 (2017-11-13 01:03), 1.18 (2018-07-06 21:30), 1.19.2 (2019-03-13 22:57), 1.19.3 (2019-05-12 21:50), 1.20 (2021-07-29 19:00), 1.21 (2021-12-23 09:52), 1.22.1 (2023-03-20 22:10), 1.22 (2022-11-10 12:00)
Other packages that cited MALDIquant R package
View MALDIquant citation profile
Other R packages that MALDIquant depends, imports, suggests or enhances
Functions, R codes and Examples using the MALDIquant R package
Some associated functions: AbstractMassObject-class . MALDIquant-defunct . MALDIquant-deprecated . MALDIquant-package . MALDIquant-parallel . MassPeaks-class . MassSpectrum-class . alignSpectra-functions . averageMassSpectra-functions . binPeaks-functions . calibrateIntensity-methods . createMassPeaks-functions . createMassSpectrum-functions . detectPeaks-methods . determineWarpingFunctions-functions . estimateBaseline-methods . estimateNoise-methods . fiedler2009subset . filterPeaks-functions . findEmptyMassObjects-functions . intensityMatrix-functions . isMassObject-functions . isMassObjectList-functions . labelPeaks-methods . match.closest . mergeMassPeaks-functions . monoisotopicPeaks-methods . msiSlices-functions . plot-methods . plotMsiSlice-methods . referencePeaks-functions . removeBaseline-methods . smoothIntensity-methods . transformIntensity-methods . trim-methods . warp-functions . 
Some associated R codes: AllClasses.R . AllGenerics.R . Deprecated.R . alignSpectra-functions.R . approxfun-methods.R . as-methods.R . as.list-functions.R . as.matrix-functions.R . as.matrix-methods.R . averageMassSpectra-functions.R . binPeaks-functions.R . calculateLabelPositions-functions.R . calibrateIntensity-functions.R . calibrateIntensity-methods.R . colMedians-functions.R . constructor-functions.R . coordinates-methods.R . deprecated-functions.R . detectPeaks-methods.R . determineWarpingFunctions-functions.R . doByLabels-functions.R . estimateBaseline-functions.R . estimateBaseline-methods.R . estimateNoise-functions.R . estimateNoise-methods.R . filterPeaks-functions.R . findEmptyMassObjects-functions.R . findLocalMaxima-methods.R . grouper-functions.R . intensity-methods.R . intensityMatrix-functions.R . irregular-functions.R . isEmpty-methods.R . isFunctionList-functions.R . isMassObject-functions.R . isMassObjectList-functions.R . isRegular-methods.R . isValidHalfWindowSize-functions.R . labelPeaks-methods.R . lapply-functions.R . length-methods.R . lines-methods.R . localMaxima-functions.R . mapply-functions.R . mass-methods.R . match.closest-functions.R . memoryUsage-functions.R . merge-functions.R . metaData-methods.R . monoisotopic-functions.R . monoisotopicPeaks-methods.R . morphologicalFilter-functions.R . msiSlices-functions.R . mz-methods.R . onAttach.R . plot-methods.R . plotMsiSlice-functions.R . plotMsiSlice-methods.R . points-methods.R . range-functions.R . referencePeaks-functions.R . removeBaseline-methods.R . removeEmptyMassObjects-functions.R . reorder-functions.R . replaceNegativeIntensityValues-functions.R . show-functions.R . show-methods.R . smoothIntensity-methods.R . smoothingFilters-functions.R . snr-methods.R . subset-methods.R . totalIonCurrent-methods.R . transformIntensity-methods.R . trim-methods.R . unlist-functions.R . valid-methods.R . warp-functions.R . warpingFunction-functions.R .  Full MALDIquant package functions and examples
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