adductomicsR

DOI: 10.18129/B9.bioc.adductomicsR    

Processing of adductomic mass spectral datasets

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") 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	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
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_1.8.0.tar.gz
Windows Binary	adductomicsR_1.8.0.zip
macOS 10.13 (High Sierra)	adductomicsR_1.8.0.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	https://bioconductor.org/packages/adductomicsR/
Package Downloads Report	Download Stats