RpsiXML

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RpsiXML.

R interface to PSI-MI 2.5 files


Bioconductor version: 3.10

Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.

Author: Jitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang

Maintainer: Jitao David Zhang <jitao_david.zhang at roche.com>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("RpsiXML")

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("RpsiXML")
Application Examples of RpsiXML package PDF R Script
Reading PSI-25 XML files PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Infrastructure, Proteomics, Software
Version 2.28.0
In Bioconductor since BioC 2.3 (R-2.8) (15.5 years)
License LGPL-3
Depends methods, annotate(>= 1.21.0), graph(>= 1.21.0), Biobase, RBGL(>= 1.17.0), XML (>= 2.4.0), hypergraph(>= 1.15.2), AnnotationDbi
Imports
System Requirements
URL http://www.bioconductor.org
See More
Suggests org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db, Rgraphviz, ppiStats, ScISI
Linking To
Enhances
Depends On Me ScISI
Imports Me ScISI
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package RpsiXML_2.28.0.tar.gz
Windows Binary RpsiXML_2.28.0.zip
Mac OS X 10.11 (El Capitan) RpsiXML_2.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RpsiXML
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RpsiXML
Bioc Package Browser https://code.bioconductor.org/browse/RpsiXML/
Package Short Url https://bioconductor.org/packages/RpsiXML/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive