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
Date/Publication: 2025-11-17
NeedsCompilation: no
Packaged: 2025-11-17 21:05:32 UTC; biocbuild
Built: R 4.6.0; ; 2025-11-18 11:47:39 UTC; unix
