MSstatsLiP

DOI: 10.18129/B9.bioc.MSstatsLiP    

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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 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 1.0.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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
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_1.0.0.tar.gz
Windows Binary MSstatsLiP_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) MSstatsLiP_1.0.0.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 3.14 Source Archive

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