adductomicsR

DOI: 10.18129/B9.bioc.adductomicsR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see adductomicsR.

Processing of adductomic mass spectral datasets

Bioconductor version: 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>

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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Imports Me
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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 [email protected]:packages/adductomicsR
Package Short Url	https://bioconductor.org/packages/adductomicsR/
Package Downloads Report	Download Stats