PepSetTest

This is the development version of PepSetTest; to use it, please install the devel version of Bioconductor.

Peptide Set Test


Bioconductor version: Development (3.20)

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, enter citation("PepSetTest")):

Installation

To install this package, start R (version "4.4") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("PepSetTest")
A Tutorial for PepSetTest HTML R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, MassSpectrometry, Proteomics, Regression, Software
Version 0.99.7
In Bioconductor since BioC 3.20 (R-4.4)
License GPL (>= 3)
Depends
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
Suggests statmod, BiocStyle, knitr, rmarkdown, tidyr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PepSetTest_0.99.7.tar.gz
Windows Binary PepSetTest_0.99.7.zip
macOS Binary (x86_64) PepSetTest_0.99.7.tgz
macOS Binary (arm64) PepSetTest_0.99.7.tgz
Source Repository git clone https://git.bioconductor.org/packages/PepSetTest
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PepSetTest
Bioc Package Browser https://code.bioconductor.org/browse/PepSetTest/
Package Short Url https://bioconductor.org/packages/PepSetTest/
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