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Bioconductor - PhosR

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)

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 "4.5") 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")
Details biocViews Proteomics, ResearchField, Software Version 1.18.1 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 Links To Me Build Report Build Report Package Archives

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

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