PepSetTest
Peptide Set Test
Bioconductor version: 3.23 · Package version: 1.6.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PepSetTest")Details
| Maintainer | Junmin Wang <jmwang.bio@gmail.com> |
| Author | Junmin Wang [aut, cre] |
| License | GPL (>= 3) |
| URL | https://github.com/JmWangBio/PepSetTest |
| Bug Reports | https://github.com/JmWangBio/PepSetTest/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, MassSpectrometry, Proteomics, Regression, Software |
| Package Short Url | https://bioconductor.org/packages/PepSetTest/ |
Citation
From within R, enter citation("PepSetTest"):
Junmin Wang. PepSetTest: Peptide Set Test. doi:10.18129/B9.bioc.PepSetTest, R package version 1.6.0, https://bioconductor.org/packages/PepSetTest.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | PepSetTest_1.6.0.tar.gz |
| Windows binary (x86_64) | PepSetTest_1.6.0.zip |
| macOS binary (arm64) | PepSetTest_1.6.0.tgz |
| macOS binary (x86_64) | PepSetTest_1.6.0.tgz |