PhosR

DOI: 10.18129/B9.bioc.PhosR  

A set of methods and tools for comprehensive analysis of phosphoproteomics data

Bioconductor version: Release (3.16)

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], Taiyun Kim [aut, cre], Hani Jieun Kim [aut]

Maintainer: Taiyun Kim <taiyun.kim91 at gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	An introduction to PhosR package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Proteomics, ResearchField, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.1.0)
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
LinkingTo
Suggests	testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	PhosR_1.8.0.tar.gz
Windows Binary	PhosR_1.8.0.zip
macOS Binary (x86_64)	PhosR_1.8.0.tgz
macOS Binary (arm64)	PhosR_1.8.0.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