PhosR
This is the development version of PhosR; for the stable release version, see PhosR.
A set of methods and tools for comprehensive analysis of phosphoproteomics data
Bioconductor version: Development (3.22)
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")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.19.2 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 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_1.19.2.tar.gz |
| Windows Binary (x86_64) | PhosR_1.19.0.zip |
| macOS Binary (x86_64) | PhosR_1.19.2.tgz |
| macOS Binary (arm64) | PhosR_1.19.2.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 |