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Bioconductor - MSstatsLiP

MSstatsLiP

This is the released version of MSstatsLiP; for the devel version, see MSstatsLiP.

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Bioconductor version: Release (3.21)

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.

Author: Devon Kohler [aut, cre], Tsung-Heng Tsai [aut], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Valentina Cappelletti [aut], Liliana Malinovska [aut], Olga Vitek [aut]

Maintainer: Devon Kohler <kohler.d at northeastern.edu>

Citation (from within R, enter citation("MSstatsLiP")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSstatsLiP")

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("MSstatsLiP")
MSstatsLiP Proteolytic Workflow HTML R Script MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package HTML R Script Reference Manual PDF Details biocViews DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel Version 1.14.1 In Bioconductor since BioC 3.14 (R-4.1) (3.5 years) License Artistic-2.0 Depends R (>= 4.1) Imports dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats, MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats System Requirements URL Bug Reports https://github.com/Vitek-Lab/MSstatsLiP/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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