hdxmsqc
This is the released version of hdxmsqc; for the devel version, see hdxmsqc.
An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
Bioconductor version: Release (3.23)
The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data.
Author: Oliver M. Crook [aut, cre]
Maintainer: Oliver M. Crook <oliver.crook at stats.ox.ac.uk>
citation("hdxmsqc")):
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("hdxmsqc")
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("hdxmsqc")| Qualityt control for differential hydrogen deuterium exchange mass spectrometry data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, MassSpectrometry, Metabolomics, Proteomics, QualityControl, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | file LICENSE |
| Depends | R (>= 4.3), QFeatures, S4Vectors, Spectra |
| Imports | dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices, stats, MsCoreUtils |
| System Requirements | |
| URL | http://github.com/ococrook/hdxmsqc |
| Bug Reports | https://github.com/ococrook/hdxmsqc/issues |
See More
| Suggests | RColorBrewer, pheatmap, MASS, patchwork, 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 | hdxmsqc_1.8.0.tar.gz |
| Windows Binary (x86_64) | hdxmsqc_1.8.0.zip |
| macOS Binary (big-sur-x86_64) | hdxmsqc_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | hdxmsqc_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/hdxmsqc |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/hdxmsqc |
| Bioc Package Browser | https://code.bioconductor.org/browse/hdxmsqc/ |
| Package Short Url | https://bioconductor.org/packages/hdxmsqc/ |
| Package Downloads Report | Download Stats |