SmartPhos
This is the development version of SmartPhos; for the stable release version, see SmartPhos.
All Bioconductor versions of SmartPhos
3.24 (devel), 3.23 (release), 3.22
A phosphoproteomics data analysis package with an interactive ShinyApp
Bioconductor version: 3.24 · Package version: 1.3.0
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] 
, Junyan Lu [aut]
Maintainer: Shubham Agrawal <shubhamagrawal2706 at gmail.com>
Citation
From within R, enter citation("SmartPhos"):
Shubham Agrawal, Junyan Lu. SmartPhos: A phosphoproteomics data analysis package with an interactive ShinyApp. doi:10.18129/B9.bioc.SmartPhos, R package version 1.3.0, https://bioconductor.org/packages/SmartPhos.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("SmartPhos")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.3.0 |
| License | GPL-3 |
| URL | https://lu-group-ukhd.github.io/SmartPhos/ |
| Bug Reports | https://github.com/Bioconductor/SmartPhos/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.22 (R-4.5) (less than a year) |
| Downloads rank | 2344 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, Clustering, DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, ShinyApps, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/SmartPhos/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SmartPhos")| SmartPhos Explorer: a one-stop data analysis platform for proteomic and phosphoproteomic data | HTML |
| SmartPhos: a pipeline for processing and analysis of phosphoproteomic data | HTML |
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Windows binary (x86_64) | SmartPhos_1.3.0.zip |
| macOS binary (arm64) | SmartPhos_1.3.0.tgz |
| macOS binary (x86_64) | SmartPhos_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SmartPhos |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SmartPhos |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.4.0)
Imports: MultiAssayExperiment, SummarizedExperiment, data.table, shiny, shinythemes, shinyjs, shinyBS, shinyWidgets, parallel, DT, tools, stats, ggplot2, plotly, ggbeeswarm, pheatmap, grid, XML, MsCoreUtils, imputeLCMD, missForest, limma, proDA, decoupleR, piano, BiocParallel, doParallel, doRNG, e1071, magrittr, matrixStats, rlang, stringr, tibble, dplyr, tidyr, Biobase, vsn, factoextra, cowplot