MSstatsLiP
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
Bioconductor version: 3.23 · Package version: 1.18.0
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 |
| Downloads rank | 464 |
| Source branch | RELEASE_3_23 |
| biocViews | DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel |
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