BioPlex

This is the development version of BioPlex; for the stable release version, see BioPlex.

R-side access to BioPlex protein-protein interaction data

Bioconductor version: Development (3.21)

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")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

1. Data retrieval	HTML	R Script
2. Data checks	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	1.13.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), SummarizedExperiment
Imports	BiocFileCache, GenomicRanges, GenomeInfoDb, 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, GenomicFeatures, S4Vectors, depmap, knitr, rmarkdown
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.

Source Package	BioPlex_1.13.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/BioPlex
Source Repository (Developer Access)	git clone [email protected]:packages/BioPlex
Package Short Url	https://bioconductor.org/packages/BioPlex/
Package Downloads Report	Download Stats