MSstats
This is the development version of MSstats; for the stable release version, see MSstats.
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Bioconductor version: Development (3.22)
A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.
Author: Meena Choi [aut, cre], Mateusz Staniak [aut], Devon Kohler [aut], Tony Wu [aut], Deril Raju [aut], Tsung-Heng Tsai [aut], Ting Huang [aut], Olga Vitek [aut]
Maintainer: Meena Choi <mnchoi67 at gmail.com>
citation("MSstats")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("MSstats")
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("MSstats")| MSstats+: Peak quality-weighted differential analysis | HTML | R Script |
| MSstats: End to End Workflow | HTML | R Script |
| MSstats: Protein/Peptide significance analysis | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Normalization, Proteomics, QualityControl, Software, TimeCourse |
| Version | 4.17.2 |
| In Bioconductor since | BioC 2.13 (R-3.0) (12 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0) |
| Imports | MSstatsConvert, data.table, checkmate, MASS, htmltools, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, plotly, marray, stats, grDevices, graphics, methods, statmod, parallel, rlang |
| System Requirements | |
| URL | http://msstats.org |
| Bug Reports | https://groups.google.com/forum/#!forum/msstats |
See More
| Suggests | BiocStyle, knitr, rmarkdown, tinytest, covr, markdown, mockery, kableExtra |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | MSstatsBioNet |
| Imports Me | artMS, MSstatsBig, MSstatsLiP, MSstatsPTM, MSstatsShiny, MSstatsTMT |
| Suggests Me | MSstatsResponse |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSstats_4.17.2.tar.gz |
| Windows Binary (x86_64) | MSstats_4.17.1.zip |
| macOS Binary (x86_64) | MSstats_4.17.2.tgz |
| macOS Binary (arm64) | MSstats_4.17.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSstats |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSstats |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSstats/ |
| Package Short Url | https://bioconductor.org/packages/MSstats/ |
| Package Downloads Report | Download Stats |