This is the development version of PepSetTest; for the stable release version, see PepSetTest.
Peptide Set TestBioconductor version: Development (3.22)
Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights.
Author: Junmin Wang [aut, cre]
Maintainer: Junmin Wang <jmwang.bio at gmail.com>
Citation (from within R, entercitation("PepSetTest")
): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("PepSetTest")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PepSetTest")
Details biocViews DifferentialExpression, MassSpectrometry, Proteomics, Regression, Software Version 1.3.0 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) License GPL (>= 3) Depends R (>= 4.1.0) Imports dplyr, limma, lme4, MASS, matrixStats, reshape2, stats, tibble, SummarizedExperiment, methods System Requirements URL https://github.com/JmWangBio/PepSetTest Bug Reports https://github.com/JmWangBio/PepSetTest/issues See More Package Archives
Follow Installation instructions to use this package in your R session.
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