adductomicsR
This is the released version of adductomicsR; for the devel version, see adductomicsR.
Processing of adductomic mass spectral datasets
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.27.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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_1.27.0.tar.gz |
| Windows Binary (x86_64) | adductomicsR_1.27.0.zip |
| macOS Binary (big-sur-x86_64) | adductomicsR_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | |
| 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 |