mspms
This is the development version of mspms; for the stable release version, see mspms.
Tools for the analysis of MSP-MS data
Bioconductor version: Development (3.24)
This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.
Author: Charlie Bayne [aut, cre]
Maintainer: Charlie Bayne <baynec2 at gmail.com>
citation("mspms")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("mspms")
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("mspms")| mspms_vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MassSpectrometry, Preprocessing, Proteomics, Software |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | QFeatures, limma, SummarizedExperiment, magrittr, rlang, dplyr, purrr, stats, tidyr, stringr, ggplot2, ggseqlogo, heatmaply, readr, rstatix, tibble, ggpubr, imputeLCMD |
| System Requirements | |
| URL | https://github.com/baynec2/mspms |
| Bug Reports | https://github.com/baynec2/mspms/issues |
See More
| Suggests | knitr, testthat (>= 3.0.0), downloadthis, DT, rmarkdown, BiocStyle |
| 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 | mspms_1.5.0.tar.gz |
| Windows Binary (x86_64) | mspms_1.5.0.zip |
| macOS Binary (big-sur-x86_64) | mspms_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | mspms_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mspms |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mspms |
| Bioc Package Browser | https://code.bioconductor.org/browse/mspms/ |
| Package Short Url | https://bioconductor.org/packages/mspms/ |
| Package Downloads Report | Download Stats |