msqrob2
This is the released version of msqrob2; for the devel version, see msqrob2.
Robust statistical inference for quantitative LC-MS proteomics
Bioconductor version: Release (3.23)
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")):Lieven Clement, Laurent Gatto, Oliver M. Crook, Stijn Vandenbulcke. msqrob2: Robust statistical inference for quantitative LC-MS proteomics. doi:10.18129/B9.bioc.msqrob2, R package version 1.20.0, https://bioconductor.org/packages/msqrob2.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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")| Introduction to proteomics data analysis - MaxQuant Data Dependent Acquisition spike-in study | HTML | R Script |
| Differential abundance analysis for Data Independent Acquistion (DIA-NN - starting from Precursor.Quantity) | HTML | R Script |
| Differential abundance analysis for Data Independent Acquistion (Spectronaut - starting from FG_MS2RawQuantity) | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ExperimentalDesign, ImmunoOncology, MassSpectrometry, Metabolomics, MultipleComparison, Normalization, Preprocessing, Proteomics, Regression, Software, TimeCourse |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 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, matrixStats, ggplot2, assertthat, dplyr, grDevices, utils, rlang |
| System Requirements | |
| URL | https://github.com/statOmics/msqrob2 |
| Bug Reports | https://github.com/statOmics/msqrob2/issues |
See More
| Suggests | stringr, ExploreModelMatrix, kableExtra, ComplexHeatmap, scater, multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, tidyr, plotly, MsDataHub, MSnbase, MsCoreUtils, covr, arrow, data.table, ggcorrplot, iq |
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| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | msqrob2_1.20.0.tar.gz |
| Windows Binary (x86_64) | msqrob2_1.20.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | msqrob2_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | msqrob2_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/msqrob2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/msqrob2 |
| Package Short Url | https://bioconductor.org/packages/msqrob2/ |
| Package Downloads Report | Download Stats |