Package: ComplexMap 2.0.0

ComplexMap: A Toolset for the Functional Analysis and Interactive Visualization of Protein Complex Data

Provides a comprehensive workflow for the quality control, refinement, functional enrichment, and network-based analysis of protein complex datasets. ComplexMap allows for the quantitative evaluation of predicted complexes against a reference and provides an interactive Cytoscape.js-powered Shiny explorer to navigate the functional landscape of a protein complex map.

Authors:Qingzhou Zhang [aut, cre]

ComplexMap_2.0.0.tar.gz
ComplexMap_2.0.0.zip(r-4.7-any)ComplexMap_2.0.0.zip(r-4.6-any)ComplexMap_2.0.0.zip(r-4.5-any)
ComplexMap_2.0.0.tgz(r-4.6-any)ComplexMap_2.0.0.tgz(r-4.5-any)
ComplexMap_2.0.0.tar.gz(r-4.7-any)ComplexMap_2.0.0.tar.gz(r-4.6-any)
ComplexMap_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ComplexMap/json (API)

# Install 'ComplexMap' in R:

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

Bug tracker:https://github.com/zqzneptune/complexmap/issues

Pkgdown/docs site:https://zqzneptune.github.io

Datasets:

demoComplexes - Example Protein Complex List
referenceComplexes - Reference Protein Complex Set

On CRAN:

3.85 score 6 scripts 24 exports 82 dependencies

Last updated from:83415bf695. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	245
source / vignettes	OK	330
linux-release	NOTE	192
macos-release	NOTE	142
macos-oldrel	NOTE	214
windows-devel	NOTE	107
windows-release	NOTE	151
windows-oldrel	NOTE	155
wasm-release	OK	210

Exports:%>%benchmarkParameters buildComplexNetwork computeMapTopology createComplexMap evaluateComplexes explore exportNetwork generateNodeAttributes getEdgeTable getExampleGmt getGmtFromFile getGoGmt getMsigdbGmt getNodeTable getReactomeGmt pruneNetwork qcComplexList queryMap refineComplexList runComplexEnrichment runComplexMapApp scaleLayoutForCytoscape toCytoscapeJSON

Dependencies:AnnotationDbi askpass assertthat babelgene base64enc Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 blob bslib cachem cli clue cluster codetools commonmark cpp11 crayon curl DBI digest dplyr fastmap fontawesome fs future future.apply generics globals glue GO.db htmltools httpuv httr igraph IRanges jquerylib jsonlite KEGGREST later lattice lifecycle listenv magrittr Matrix memoise mime msigdbr openssl otel parallelly pillar pkgconfig png promises purrr R6 rappdirs RColorBrewer Rcpp reactome.db rlang RSQLite S4Vectors sass Seqinfo shiny sourcetools stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr xtable XVector

Start a Typical Workflow

Rendered fromvignette_02-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-02-19
Started: 2025-11-11

Preparing Your Input Data

The ComplexMap Philosophy: Identifier Matching | Preparing Functional Gene Sets (GMT) | Method 1: From a User-Provided Local File | Method 2: From the Molecular Signatures Database (MSigDB) | Method 3: From Gene Ontology (GO) via Bioconductor | Method 4: From Reactome Pathways via Bioconductor

Rendered fromvignette_01-prep-input.Rmdusingknitr::rmarkdown

Last update: 2025-12-03
Started: 2025-11-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Benchmark Complex Refinement Parameters	benchmarkParameters
Build a Complex-Complex Interaction Network	buildComplexNetwork
Compute Network Topology and Layout Coordinates	computeMapTopology
Create a Complete Complex Map Object	createComplexMap
Example Protein Complex List	demoComplexes
Evaluate Predicted Protein Complexes Against a Reference Set	evaluateComplexes
Explore a ComplexMap Object Interactively	explore
Export a ComplexMap Network for External Tools	exportNetwork
Generate Node Attributes for a Complex Network	generateNodeAttributes
Get the Edge Table from a ComplexMap Object	getEdgeTable
Get the Path to an Example GMT File	getExampleGmt
Read a GMT File from a Local Path	getGmtFromFile
Fetch Gene Ontology (GO) Gene Sets	getGoGmt
Fetch Gene Sets from MSigDB	getMsigdbGmt
Get the Node Table from a ComplexMap Object	getNodeTable
Fetch Reactome Pathway Gene Sets	getReactomeGmt
Print Method for a ComplexMap Object	print.ComplexMap
Prune Network Edges Before Cytoscape Export	pruneNetwork
Perform Quality Control on a List of Protein Complexes	qcComplexList
Query a ComplexMap Object	queryMap
Reference Protein Complex Set (CORUM)	referenceComplexes
Refine a List of Protein Complexes by Size and Redundancy	refineComplexList
Run Gene Set Enrichment Analysis on a List of Complexes	runComplexEnrichment
Run the ComplexMap Interactive Explorer	runComplexMapApp
Scale Layout Coordinates for Cytoscape.js	scaleLayoutForCytoscape
Export a ComplexMap Object to Cytoscape.js JSON	toCytoscapeJSON