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PhosR

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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 Proteomics, ResearchField, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
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Suggests testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate
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Package Archives

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

Source Package PhosR_1.12.0.tar.gz
Windows Binary PhosR_1.12.0.zip
macOS Binary (x86_64) PhosR_1.12.0.tgz
macOS Binary (arm64) PhosR_1.12.0.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