PepSetTest
Peptide Set Test
Bioconductor version: Release (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("PepSetTest")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 |
Details
| biocViews | DifferentialExpression, MassSpectrometry, Proteomics, Regression, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| 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 |
| 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 | PepSetTest_1.0.0.tar.gz |
| Windows Binary (x86_64) | PepSetTest_1.0.0.zip |
| macOS Binary (x86_64) | PepSetTest_1.0.0.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/ |
| Package Downloads Report | Download Stats |