MSstatsLiP

DOI: 10.18129/B9.bioc.MSstatsLiP    

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	MSstatsLiP Proteolytic Workflow
HTML	R Script	MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package
PDF		Reference Manual

Details

biocViews	DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version	1.2.1
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
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
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
SystemRequirements
Enhances
URL
BugReports	https://github.com/Vitek-Lab/MSstatsLiP/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MSstatsLiP_1.2.1.tar.gz
Windows Binary	MSstatsLiP_1.2.1.zip (64-bit only)
macOS Binary (x86_64)	MSstatsLiP_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSstatsLiP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSstatsLiP
Package Short Url	https://bioconductor.org/packages/MSstatsLiP/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive