adductomicsR

DOI: 10.18129/B9.bioc.adductomicsR    

Processing of adductomic mass spectral datasets

Bioconductor version: Release (3.9)

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.

Author: Josie Hayes <jlhayes1982 at gmail.com>

Maintainer: Josie Hayes <jlhayes1982 at gmail.com>

Citation (from within R, enter citation("adductomicsR")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("adductomicsR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("adductomicsR")

 

HTML R Script Adductomics workflow
PDF   Reference Manual

Details

biocViews DataImport, GUI, MassSpectrometry, Metabolomics, Software, ThirdPartyClient
Version 1.0.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License Artistic-2.0
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)
LinkingTo
Suggests knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop(>= 1.34.0), testthat
SystemRequirements
Enhances
URL
BugReports https://github.com/JosieLHayes/adductomicsR/issues
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package adductomicsR_1.0.0.tar.gz
Windows Binary adductomicsR_1.0.0.zip
Mac OS X 10.11 (El Capitan) adductomicsR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/adductomicsR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/adductomicsR
Package Short Url http://bioconductor.org/packages/adductomicsR/
Package Downloads Report Download Stats

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