BioPlex

This is the released version of BioPlex; for the devel version, see BioPlex.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14

R-side access to BioPlex protein-protein interaction data

Bioconductor version: Release (3.23)

The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data.

Author: Ludwig Geistlinger [aut, cre], Robert Gentleman [aut]

Maintainer: Ludwig Geistlinger <ludwig_geistlinger at hms.harvard.edu>

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

Ludwig Geistlinger, Robert Gentleman. BioPlex: R-side access to BioPlex protein-protein interaction data. doi:10.18129/B9.bioc.BioPlex, R package version 1.18.0, https://bioconductor.org/packages/BioPlex.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("BioPlex")

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("BioPlex")

2. Data checks	HTML	R Script
1. Data retrieval	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellCulture, ColonCancerData, ExperimentData, ExperimentHub, ExpressionData, GEO, Genome, Homo_sapiens_Data, MassSpectrometryData, Proteome, RNASeqData, ReproducibleResearch
Version	1.18.0
In Bioconductor since	BioC 3.14 (R-4.1) (5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), SummarizedExperiment
Imports	BiocFileCache, GEOquery, graph, methods, utils
System Requirements
URL	https://github.com/ccb-hms/BioPlex
Bug Reports	https://github.com/ccb-hms/BioPlex/issues

Suggests	AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, depmap, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	BioPlex_1.18.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/BioPlex
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BioPlex
Package Short Url	https://bioconductor.org/packages/BioPlex/
Package Downloads Report	Download Stats