MSstatsPTM
This is the development version of MSstatsPTM; for the stable release version, see MSstatsPTM.
Statistical Characterization of Post-translational Modifications
Bioconductor version: Development (3.24)
MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.
Author: Devon Kohler [aut], Tsung-Heng Tsai [aut], Anthony Wu [aut, cre], Deril Raju [aut], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Olga Vitek [aut]
Maintainer: Anthony Wu <wu.anthon at northeastern.edu>
citation("MSstatsPTM")):
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("MSstatsPTM")
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("MSstatsPTM")| MSstatsPTM LabelFree Workflow | HTML | R Script |
| MSstatsPTM TMT Workflow | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel |
| Version | 2.15.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3) |
| Imports | dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices, MSstatsTMT, MSstatsConvert(>= 1.19.1), MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel, plotly, htmltools, rlang |
| System Requirements | |
| URL | https://vitek-lab.github.io/MSstatsPTM/ |
| Bug Reports | https://github.com/Vitek-Lab/MSstatsPTM/issues |
See More
| Suggests | knitr, rmarkdown, tinytest, covr, mockery, arrow, testthat (>= 3.0.0) |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | MSstatsLiP, 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 | MSstatsPTM_2.15.0.tar.gz |
| Windows Binary (x86_64) | MSstatsPTM_2.15.0.zip |
| macOS Binary (big-sur-x86_64) | MSstatsPTM_2.15.0.tgz |
| macOS Binary (sonoma-arm64) | MSstatsPTM_2.15.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSstatsPTM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSstatsPTM |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSstatsPTM/ |
| Package Short Url | https://bioconductor.org/packages/MSstatsPTM/ |
| Package Downloads Report | Download Stats |