msqrob2

DOI: 10.18129/B9.bioc.msqrob2  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see msqrob2.

Robust statistical inference for quantitative LC-MS proteomics

Bioconductor version: 3.17

msqrob2 provides a robust linear mixed model framework for assessing differential abundance in MS-based Quantitative proteomics experiments. Our workflows can start from raw peptide intensities or summarised protein expression values. The model parameter estimates can be stabilized by ridge regression, empirical Bayes variance estimation and robust M-estimation. msqrob2's hurde workflow can handle missing data without having to rely on hard-to-verify imputation assumptions, and, outcompetes state-of-the-art methods with and without imputation for both high and low missingness. It builds on QFeature infrastructure for quantitative mass spectrometry data to store the model results together with the raw data and preprocessed data.

Author: Lieven Clement [aut, cre] , Laurent Gatto [aut] , Oliver M. Crook [aut] , Adriaan Sticker [ctb], Ludger Goeminne [ctb], Milan Malfait [ctb] , Stijn Vandenbulcke [aut]

Maintainer: Lieven Clement <lieven.clement at ugent.be>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("msqrob2")

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("msqrob2")

 

HTML	R Script	A. label-free workflow with two group design
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, ExperimentalDesign, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Preprocessing, Proteomics, Regression, Software, TimeCourse
Version	1.8.0
In Bioconductor since	BioC 3.13 (R-4.1) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.1), QFeatures(>= 1.1.2)
Imports	stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools
LinkingTo
Suggests	multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr
SystemRequirements
Enhances
URL	https://github.com/statOmics/msqrob2
BugReports	https://github.com/statOmics/msqrob2/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	msqrob2_1.8.0.tar.gz
Windows Binary	msqrob2_1.8.0.zip
macOS Binary (x86_64)	msqrob2_1.8.0.tgz
macOS Binary (arm64)	msqrob2_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/msqrob2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/msqrob2
Bioc Package Browser	https://code.bioconductor.org/browse/msqrob2/
Package Short Url	https://bioconductor.org/packages/msqrob2/
Package Downloads Report	Download Stats