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adductomicsR

This is the development version of adductomicsR; for the stable release version, see adductomicsR.

Processing of adductomic mass spectral datasets


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Adductomics workflow HTML R Script
Reference Manual PDF

Details

biocViews DataImport, GUI, MassSpectrometry, Metabolomics, Software, ThirdPartyClient
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (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)
System Requirements
URL
Bug Reports https://github.com/JosieLHayes/adductomicsR/issues
See More
Suggests knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop(>= 1.34.0), testthat
Linking To
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Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package adductomicsR_1.19.0.tar.gz
Windows Binary adductomicsR_1.19.0.zip
macOS Binary (x86_64) adductomicsR_1.19.0.tgz
macOS Binary (arm64) adductomicsR_1.19.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/adductomicsR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/adductomicsR
Bioc Package Browser https://code.bioconductor.org/browse/adductomicsR/
Package Short Url https://bioconductor.org/packages/adductomicsR/
Package Downloads Report Download Stats