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BioPlex

R-side access to BioPlex protein-protein interaction data

Bioconductor version: Release (3.17)

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 "4.3") 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")
1. Data retrieval HTML R Script
2. Data checks HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellCulture, ColonCancerData, ExperimentData, ExperimentHub, ExpressionData, GEO, Genome, Homo_sapiens_Data, MassSpectrometryData, Proteome, RNASeqData, ReproducibleResearch
Version 1.6.0
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License Artistic-2.0
Depends R (>= 4.1.0), SummarizedExperiment
Imports BiocFileCache, GenomicRanges, GenomeInfoDb, GEOquery, graph, methods, utils
Linking To
Suggests AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr, rmarkdown
System Requirements
Enhances
URL https://github.com/ccb-hms/BioPlex
Bug Reports https://github.com/ccb-hms/BioPlex/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package BioPlex_1.6.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (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