PhosR
This is thereleased version of PhosR; for the devel version, seePhosR.
A set of methods and tools for comprehensive analysis of phosphoproteomics data
Bioconductor version: Release (3.22)
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], Di Xiao [aut, cre], Hani Jieun Kim [aut]
Maintainer: Di Xiao <di.xiao at sydney.edu.au>
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 appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Proteomics,ResearchField,Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| License | GPL-3 + fileLICENSE |
| 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 | SmartPhos |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | PhosR_1.20.0.tar.gz |
| Windows Binary (x86_64) | PhosR_1.20.0.zip |
| macOS Binary (x86_64) | PhosR_1.20.0.tgz |
| macOS Binary (arm64) | PhosR_1.20.0.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 |