MSstatsTMT
This is the released version of MSstatsTMT; for the devel version, see MSstatsTMT.
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Bioconductor version: Release (3.23)
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], Tony Wu [aut], Deril Raju [aut], Sicheng Hao [aut], Olga Vitek [aut]
Maintainer: Devon Kohler <kohler.d at northeastern.edu>
citation("MSstatsTMT")):Devon Kohler, Ting Huang, Meena Choi, Mateusz Staniak, Tony Wu, Deril Raju, Sicheng Hao, Olga Vitek. MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. doi:10.18129/B9.bioc.MSstatsTMT, R package version 2.20.0, https://bioconductor.org/packages/MSstatsTMT.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | 2.20.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 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 | MSstatsResponse |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSstatsTMT_2.20.0.tar.gz |
| Windows Binary (x86_64) | MSstatsTMT_2.20.0.zip |
| macOS Binary (big-sur-x86_64) | MSstatsTMT_2.20.0.tgz |
| macOS Binary (sonoma-arm64) | MSstatsTMT_2.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSstatsTMT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSstatsTMT |
| Package Short Url | https://bioconductor.org/packages/MSstatsTMT/ |
| Package Downloads Report | Download Stats |