MSstatsTMTPTM
This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MSstatsTMTPTM.
Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Bioconductor version: 3.12
Tools for Post Translational Modification (PTM) and protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. The functions in this package should be used after PTM/protein summarization. They can be used to both plot the summarized results and model the summarized datasets.
Author: Devon Kohler [aut, cre], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Tsung-Heng Tsai [aut], Olga Vitek [aut]
Maintainer: Devon Kohler <kohler.d at northeastern.edu>
citation("MSstatsTMTPTM")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MSstatsTMTPTM")
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("MSstatsTMTPTM")| MSstatsTMTPTM : A package for post translational modification (PTM) significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling | HTML | R Script |
| MSstatsTMTPTM.Workflow.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0) |
| Imports | dplyr, gridExtra, stringr, reshape2, stats, utils, ggplot2, grDevices, graphics, MSstatsTMT, Rcpp |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/Vitek-Lab/MSstatsTMTPTM/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, MSstats, covr |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSstatsTMTPTM_1.0.2.tar.gz |
| Windows Binary | MSstatsTMTPTM_1.0.2.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | MSstatsTMTPTM_1.0.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSstatsTMTPTM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSstatsTMTPTM |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSstatsTMTPTM/ |
| Package Short Url | https://bioconductor.org/packages/MSstatsTMTPTM/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |