msqrob2
Robust statistical inference for quantitative LC-MS proteomics
Bioconductor version: Release (3.19)
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("msqrob2")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ExperimentalDesign, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Preprocessing, Proteomics, Regression, Software, TimeCourse |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
| 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | msqrob2_1.12.0.zip |
| macOS Binary (x86_64) | msqrob2_1.12.0.tgz |
| macOS Binary (arm64) | msqrob2_1.12.0.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 |