SmartPhos
This is thereleased version of SmartPhos; for the devel version, seeSmartPhos.
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: 0009-0005-2630-9342, Junyan Lu [aut] 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 appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SmartPhos")| Introduction to Shiny App | HTML | R Script |
| Introduction to SmartPhos | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect,Clustering,DifferentialExpression,GUI,GeneExpression,GeneSetEnrichment,MassSpectrometry,Normalization,Preprocessing,Proteomics,QualityControl,ShinyApps,Software,Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | GPL-3 |
| 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 |
| System Requirements | |
| URL | https://lu-group-ukhd.github.io/SmartPhos/ |
| Bug Reports | https://github.com/Bioconductor/SmartPhos/issues |
See More
| Suggests | knitr,BiocStyle,PhosR,testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | SmartPhos_1.0.0.tar.gz |
| Windows Binary (x86_64) | SmartPhos_1.0.0.zip |
| macOS Binary (x86_64) | SmartPhos_1.0.0.tgz |
| macOS Binary (arm64) | SmartPhos_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SmartPhos |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SmartPhos |
| Bioc Package Browser | https://code.bioconductor.org/browse/SmartPhos/ |
| Package Short Url | https://bioconductor.org/packages/SmartPhos/ |
| Package Downloads Report | Download Stats |