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 (3.24)
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")):
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("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 | 2.21.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSstatsTMT_2.21.0.tar.gz |
| Windows Binary (x86_64) | MSstatsTMT_2.21.0.zip |
| macOS Binary (big-sur-x86_64) | MSstatsTMT_2.21.0.tgz |
| macOS Binary (sonoma-arm64) | MSstatsTMT_2.21.0.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 |