MSstatsLiP
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
Bioconductor version: 3.23 · Package version: 1.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MSstatsLiP")Details
| Maintainer | Anthony Wu <wu.anthon@northeastern.edu> |
| Author | Devon Kohler [aut], Anthony Wu [aut, cre], Tsung-Heng Tsai [aut], Deril Raju [aut], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Valentina Cappelletti [aut], Liliana Malinovska [aut], Olga Vitek [aut] |
| License | Artistic-2.0 |
| Bug Reports | https://github.com/Vitek-Lab/MSstatsLiP/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel |
| Package Short Url | https://bioconductor.org/packages/MSstatsLiP/ |
Citation
From within R, enter citation("MSstatsLiP"):
Devon Kohler, Anthony Wu, Tsung-Heng Tsai, Deril Raju, Ting Huang, Mateusz Staniak, Meena Choi, Valentina Cappelletti, Liliana Malinovska, Olga Vitek. MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments. doi:10.18129/B9.bioc.MSstatsLiP, R package version 1.18.0, https://bioconductor.org/packages/MSstatsLiP.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Proteolytic resistance analysis
- MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package
Download
Follow the installation instructions to use this package in your R session.
| Source package | MSstatsLiP_1.18.0.tar.gz |
| Windows binary (x86_64) | MSstatsLiP_1.18.0.zip |
| macOS binary (arm64) | MSstatsLiP_1.18.0.tgz |
| macOS binary (x86_64) | MSstatsLiP_1.18.0.tgz |
Dependencies
Depends: R (>= 4.1)
Imports: dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats, MSstatsConvert, data.table, Biostrings, MSstatsPTM (>= 2.12.0), Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats, plotly, htmltools
LinkingTo: Rcpp
Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight