SmartPhos
This is the development version of SmartPhos; for the stable release version, see SmartPhos.
A phosphoproteomics data analysis package with an interactive ShinyApp
Bioconductor version: Development (3.24)
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("SmartPhos")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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.
Documentation
| Reference Manual |
Details
| biocViews | BatchEffect, Clustering, DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, ShinyApps, Software, Visualization |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | SmartPhos_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | SmartPhos_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | 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 Short Url | https://bioconductor.org/packages/SmartPhos/ |
| Package Downloads Report | Download Stats |