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MSstatsLiP

This is the development version of MSstatsLiP; for the stable release version, see MSstatsLiP.

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.7.0
In Bioconductor since BioC 3.14 (R-4.1) (2 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
Linking To Rcpp
Suggests BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
System Requirements
Enhances
URL
Bug Reports https://github.com/Vitek-Lab/MSstatsLiP/issues
See More
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_1.7.0.tar.gz
Windows Binary MSstatsLiP_1.7.0.zip
macOS Binary (x86_64) MSstatsLiP_1.7.0.tgz
macOS Binary (arm64) MSstatsLiP_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSstatsLiP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSstatsLiP
Bioc Package Browser https://code.bioconductor.org/browse/MSstatsLiP/
Package Short Url https://bioconductor.org/packages/MSstatsLiP/
Package Downloads Report Download Stats