adductomicsR

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see adductomicsR.

Processing of adductomic mass spectral datasets

Bioconductor version: 3.12

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 "4.0") and enter:


if (!require("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")

Adductomics workflow HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, GUI, MassSpectrometry, Metabolomics, Software, ThirdPartyClient

Version 1.6.0

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

Suggests knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop(>= 1.34.0), testthat

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