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>
citation("adductomicsR")):
Installation
To install this package, start R (version "3.6") 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 |
Details
| biocViews | DataImport, GUI, MassSpectrometry, Metabolomics, Software, ThirdPartyClient |
| Version | 1.0.0 |
| 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 | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/adductomicsR/ |
| Package Short Url | https://bioconductor.org/packages/adductomicsR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |