BioPlex
R-side access to BioPlex protein-protein interaction data
Bioconductor version: Release (3.20)
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("BioPlex")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | CellCulture, ColonCancerData, ExperimentData, ExperimentHub, ExpressionData, GEO, Genome, Homo_sapiens_Data, MassSpectrometryData, Proteome, RNASeqData, ReproducibleResearch |
| Version | 1.12.0 |
| 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 |
See More
| 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_1.12.0.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 git@git.bioconductor.org:packages/BioPlex |
| Package Short Url | https://bioconductor.org/packages/BioPlex/ |
| Package Downloads Report | Download Stats |