Bioconductor release scheduled for October 29

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 (3.21)

Comprehensive analysis of phosphoproteomics data. Provides methods and tools for filtering, imputation, normalisation, and downstream functional analysis to infer active kinases and signalling pathways.

Author: Di Xiao [aut, cre], Pengyi Yang [aut], Hani Jieun Kim [aut]

Maintainer: Di Xiao <di.xiao at sydney.edu.au>

Citation (from within R, enter citation("PhosR")):

Installation

To install this package, start R (version "4.5") 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 PDF
NEWS Text
LICENSE Text

Details

biocViews Pathways, Proteomics, ResearchField, Software
Version 1.18.5
In Bioconductor since BioC 3.12 (R-4.0) (5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.3.0)
Imports BiocGenerics, circlize, dendextend, dplyr, e1071, GGally, ggdendro, ggplot2, ggpubr, ggtext, graphics, grDevices, igraph, limma, methods, network, pcaMethods, pheatmap, preprocessCore, RColorBrewer, reshape2, rlang, ruv, S4Vectors, stats, stringi, SummarizedExperiment, tidyr, utils
System Requirements
URL https://bioconductor.org/packages/PhosR https://github.com/PYangLab/PhosR
Bug Reports https://github.com/PYangLab/PhosR/issues
See More
Suggests annotate, BiocStyle, calibrate, ClueR, directPA, knitr, org.Mm.eg.db, org.Rn.eg.db, reactome.db, rgl, rmarkdown, sna, stringr, 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 PhosR_1.18.5.tar.gz
Windows Binary (x86_64) PhosR_1.18.1.zip
macOS Binary (x86_64) PhosR_1.18.5.tgz
macOS Binary (arm64) PhosR_1.18.5.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
Old Source Packages for BioC 3.21 Source Archive