PhosR
This is the released version of PhosR; for the devel version, see PhosR.
A set of methods and tools for comprehensive analysis of phosphoproteomics data
Bioconductor version: Release (3.23)
PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.
Author: Pengyi Yang [aut], Di Xiao [aut, cre], Hani Jieun Kim [aut]
Maintainer: Di Xiao <di.xiao at sydney.edu.au>
citation("PhosR")):
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")
BiocManager::install("PhosR")
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("PhosR")| An introduction to PhosR package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Proteomics, ResearchField, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.2.0) |
| Imports | ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi |
| System Requirements | |
| URL |
See More
| Suggests | testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | SmartPhos |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PhosR_1.22.0.tar.gz |
| Windows Binary (x86_64) | PhosR_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | PhosR_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | PhosR_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PhosR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PhosR |
| Bioc Package Browser | https://code.bioconductor.org/browse/PhosR/ |
| Package Short Url | https://bioconductor.org/packages/PhosR/ |
| Package Downloads Report | Download Stats |