Welcome to the new bioconductor.org!

msqrob2

Robust statistical inference for quantitative LC-MS proteomics


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("msqrob2")):

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

Details

biocViews DifferentialExpression, ExperimentalDesign, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Preprocessing, Proteomics, Regression, Software, TimeCourse
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
System Requirements
URL https://github.com/statOmics/msqrob2
Bug Reports https://github.com/statOmics/msqrob2/issues
See More
Suggests multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr
Linking To
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 msqrob2_1.10.0.tar.gz
Windows Binary msqrob2_1.10.0.zip
macOS Binary (x86_64) msqrob2_1.10.0.tgz
macOS Binary (arm64) msqrob2_1.10.0.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