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SmartPhos
This is the released version of SmartPhos; for the devel version, see SmartPhos.
A phosphoproteomics data analysis package with an interactive ShinyApp
Bioconductor version: Release (3.22)
To facilitate and streamline phosphoproteomics data analysis, we developed SmartPhos, an R package for the pre-processing, quality control, and exploratory analysis of phosphoproteomics data generated by MaxQuant and Spectronaut. The package can be used either through the R command line or through an interactive ShinyApp called SmartPhos Explorer. The package contains methods such as normalization and normalization correction, transformation, imputation, batch effect correction, PCA, heatmap, differential expression, time-series clustering, gene set enrichment analysis, and kinase activity inference.
Author: Shubham Agrawal [aut, cre] ORCID iD ORCID: 0009-0005-2630-9342 , Junyan Lu [aut] ORCID iD ORCID: 0000-0002-9211-0746
Maintainer: Shubham Agrawal <shubhamagrawal2706 at gmail.com>
citation("SmartPhos")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SmartPhos")
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("SmartPhos")
Details
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Follow Installation instructions to use this package in your R session.