Package: adductomicsR
Type: Package
Title: Processing of adductomic mass spectral datasets
Version: 1.27.0
Date: 2019-04-12
Author: Josie Hayes <jlhayes1982@gmail.com>
Maintainer: Josie Hayes <jlhayes1982@gmail.com>
Description: Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks. 
Depends: R (>= 3.6),
    adductData,
    ExperimentHub,
    AnnotationHub 
Imports: parallel (>= 3.3.2),
	data.table (>= 1.10.4),
	OrgMassSpecR (>= 0.4.6),
	foreach (>= 1.4.3),
	mzR (>= 2.14.0),
	ade4 (>= 1.7.6),
	rvest (>= 0.3.2),
	pastecs (>= 1.3.18),
	reshape2 (>= 1.4.2),
	pracma (>= 2.0.4),
	DT (>= 0.2),
	fpc (>= 2.1.10),
	doSNOW (>= 1.0.14),
	fastcluster (>= 1.1.22),
	RcppEigen (>= 0.3.3.3.0),
	bootstrap (>= 2017.2),
	smoother (>= 1.1),
	dplyr (>= 0.7.5),
	zoo (>= 1.8),
	stats (>= 3.5.0),
	utils (>= 3.5.0),
	graphics (>= 3.5.0),
	grDevices (>= 3.5.0),
	methods (>= 3.5.0),
	datasets (>= 3.5.0)
License: Artistic-2.0
biocViews: MassSpectrometry,Metabolomics,Software,ThirdPartyClient,DataImport,
 GUI
RoxygenNote: 6.1.0
Suggests: knitr (>= 1.15.1),
	rmarkdown (>= 1.5),
	Rdisop (>= 1.34.0),
	testthat
VignetteBuilder: knitr
Collate: 
    '00AdductSpec-class.R'
    '00AdductQuantif-class.R'
    'IsotopicDistributionMod.R'
    'adductQuant.R'
    'adductSpecGen.R'
    'digestMod.R'
    'dotProdMatrix.R'
    'dotProdSpectra.R'
    'dynamicNoiseFilter.R'
    'filterAdductTable.R'
    'findPeaks.R'
    'generateTargTable.R'
    'loessWrapperMod.R'
    'ms2Group.R'
    'nAdjPeaks.R'
    'outputPeakTable.R'
    'peakIdQuant_newMethod.R'
    'peakIntegrate.R'
    'peakListId.R'
    'peakRangeSum.R'
    'probPeaks.R'
    'retentionCorr.R'
    'rtDevModelSave.R'
    'rtDevModelling.R'
    'signalGrouping.R'
    'specSimPepId.R'
    'spectraCreate.R'
    'truePeakTrough.R'
BugReports: https://github.com/JosieLHayes/adductomicsR/issues
git_url: https://git.bioconductor.org/packages/adductomicsR
git_branch: devel
git_last_commit: 3e2ced8
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
