MSstatsTMT
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see MSstatsTMT.
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Bioconductor version: 3.19
The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It provides multiple functionalities, including aata visualization, protein quantification and normalization, and statistical modeling and inference. Furthermore, it is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.
Author: Devon Kohler [aut, cre], Ting Huang [aut], Meena Choi [aut], Mateusz Staniak [aut], Sicheng Hao [aut], Olga Vitek [aut]
Maintainer: Devon Kohler <kohler.d at northeastern.edu>
citation("MSstatsTMT")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MSstatsTMT")
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("MSstatsTMT")| MSstatsTMT User Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Proteomics, Software |
| Version | 2.12.1 |
| In Bioconductor since | BioC 3.8 (R-3.5) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2) |
| Imports | limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate, plotly, htmltools |
| System Requirements | |
| URL | http://msstats.org/msstatstmt/ |
| Bug Reports | https://groups.google.com/forum/#!forum/msstats |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MSstatsPTM, MSstatsShiny |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSstatsTMT_2.12.1.tar.gz |
| Windows Binary (x86_64) | MSstatsTMT_2.12.1.zip |
| macOS Binary (x86_64) | MSstatsTMT_2.12.1.tgz |
| macOS Binary (arm64) | MSstatsTMT_2.12.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSstatsTMT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSstatsTMT |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSstatsTMT/ |
| Package Short Url | https://bioconductor.org/packages/MSstatsTMT/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |