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 (3.24)
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")):
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("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: Metabolomics workflow with MZMine | 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 | 4.21.1 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0) |
| Imports | MSstatsConvert, data.table, checkmate, MASS, htmltools, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2 (>= 3.4.0), 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, 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_4.21.1.tar.gz |
| Windows Binary (x86_64) | MSstats_4.21.0.zip |
| macOS Binary (big-sur-x86_64) | MSstats_4.21.1.tgz |
| macOS Binary (sonoma-arm64) | MSstats_4.21.1.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 |