MSstatsTMT
This is the development version of MSstatsTMT; for the stable release version, see MSstatsTMT.
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Bioconductor version: Development (3.21)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("MSstatsTMT")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
Reference Manual |
Details
biocViews | ImmunoOncology, MassSpectrometry, Proteomics, Software |
Version | 2.15.0 |
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 | |
Suggests Me | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
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 |