mspms

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see mspms.

Tools for the analysis of MSP-MS data

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0003-1870-5298

Maintainer: Charlie Bayne <baynec2 at gmail.com>

Citation (from within R, enter citation("mspms")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
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 PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews MassSpectrometry, Preprocessing, Proteomics, Software

Version 1.0.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 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

System Requirements

URL https://github.com/baynec2/mspms

Bug Reports https://github.com/baynec2/mspms/issues

Suggests knitr, testthat (>= 3.0.0), downloadthis, DT, rmarkdown, BiocStyle, imputeLCMD

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package mspms_1.0.0.tar.gz

Windows Binary (x86_64) mspms_1.0.0.zip

macOS Binary (x86_64) mspms_1.0.0.tgz

macOS Binary (arm64) mspms_1.0.0.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/

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