MSstatsLiP

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

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.MSstatsLiP

Bioconductor version: Release (3.22)

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], 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]

Maintainer: Anthony Wu <wu.anthon 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel

Version 1.16.0

In Bioconductor since BioC 3.14 (R-4.1) (4 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, plotly, htmltools

System Requirements

URL

Bug Reports https://github.com/Vitek-Lab/MSstatsLiP/issues

Suggests BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight

Linking To Rcpp

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package MSstatsLiP_1.16.0.tar.gz

Windows Binary (x86_64) MSstatsLiP_1.16.0.zip

macOS Binary (x86_64) MSstatsLiP_1.16.0.tgz

macOS Binary (arm64) MSstatsLiP_1.16.0.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