PhosR

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see PhosR.

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

Bioconductor version: 3.19

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Proteomics, ResearchField, Software

Version 1.14.0

In Bioconductor since BioC 3.12 (R-4.0) (4 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

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_1.14.0.tar.gz

Windows Binary (x86_64) PhosR_1.14.0.zip

macOS Binary (x86_64) PhosR_1.14.0.tgz

macOS Binary (arm64) PhosR_1.14.0.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/

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