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PhosR

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

Bioconductor version: 3.23 · Package version: 1.22.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PhosR")

Details

MaintainerDi Xiao <di.xiao@sydney.edu.au>
AuthorPengyi Yang [aut], Di Xiao [aut, cre], Hani Jieun Kim [aut]
LicenseGPL-3 + file LICENSE
Downloads rank451
Source branchRELEASE_3_23
biocViewsProteomics, ResearchField, Software

Documentation

Download

Dependencies

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

Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate

Reverse dependencies

Suggests Me (1): SmartPhos