Package: BioPlex 1.18.0

Ludwig Geistlinger

BioPlex: R-side access to BioPlex protein-protein interaction data

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.

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

BioPlex_1.18.0.tar.gz
BioPlex_1.18.0.tar.gz(r-4.7-any)BioPlex_1.18.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BioPlex/json (API)

# Install 'BioPlex' in R:

install.packages('BioPlex', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ccb-hms/bioplex/issues

On BioConductor:BioPlex-1.19.0(data/experiment 3.24)BioPlex-1.18.0(data/experiment 3.23)

cellculture coloncancerdata experimenthub expressiondata geo genome homo_sapiens_data massspectrometrydata proteome reproducibleresearch rnaseqdata datapkg

6.94 score 8 stars 18 scripts 84 mentions 11 exports 76 dependencies

Last updated from:a976b809e9 (on RELEASE_3_23). Checks:3 NOTE, 1 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	NOTE	168
linux-devel	NOTE	363
source / vignettes	OK	379
linux-release	NOTE	431

Exports:annotatePFAM bioplex2graph ccleProteome2SummarizedExperiment corum2graphlist corum2list getBioPlex getBioplexProteome getCorum getGSE122425 hasSubunit mapSummarizedExperimentOntoGraph

Dependencies:abind askpass Biobase BiocFileCache BiocGenerics bit bit64 blob cachem cli clipr cpp11 crayon curl data.table DBI dbplyr DelayedArray dplyr fastmap filelock generics GenomicRanges GEOquery glue graph hms httr httr2 IRanges jsonlite lattice lifecycle limma magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig prettyunits progress purrr R.methodsS3 R.oo R.utils R6 readr rentrez rlang RSQLite rvest S4Arrays S4Vectors selectr Seqinfo SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr XML xml2 XVector

Import and representation of BioPlex PPI data and related resources

Rendered fromBioPlex.Rmdusingknitr::rmarkdown

Last update: 2026-01-27
Started: 2021-02-16

Basic checks of BioPlex PPI data

Setup | Check: identify CORUM complexes that have a subunit of interest | Check: extract BioPlex PPIs for a CORUM complex | Check: identify interacting domains for a PFAM domain of interest | Check: expressed genes are showing up as prey (293T cells) | Check: is there a relationship between prey frequency and prey expression level? | Check: differential protein expression (HEK293 vs. HCT116) | SessionInfo

Rendered fromBasicChecks.Rmdusingknitr::rmarkdown

Last update: 2026-01-27
Started: 2021-04-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate PFAM domains to BioPlex PPI graph	annotatePFAM
Representation of BioPlex PPIs in a graph data structure	bioplex2graph
Convenient access to the CCLE proteome data	ccleProteome2SummarizedExperiment
Represent CORUM protein complex data as a list of graph instances	corum2graphlist
Represent CORUM protein complex data as a simple list	corum2list
Obtain BioPlex protein-protein interaction data	getBioPlex
Obtain BioPlex3 proteome data	getBioplexProteome
Obtain CORUM protein complex data	getCorum
Convenient access to 293T transcriptome data from GEO	getGSE122425
Identify CORUM complexes that have a subunit of interest	hasSubunit
Map experimental data onto a graph	mapSummarizedExperimentOntoGraph