Table 2. Top 31 network-related Bioconductor packages ordered by rank (as of Sept 2019) and their network models relevant to RCy3.
RCy3 can provide and consume network models to and from these packages (checkmarks). Asterisks indicate where a Cytoscape app is required (* aMatReader, ** WikiPathways).
| Package | Description | Network model | RCy3 |
|---|---|---|---|
| graph | Essential graph data structures | graphNEL | ✔ |
| RBGL | Graph algorithms contained in the BOOST library | graphNEL | ✔ |
| Rgraphviz | Plotting with graphviz library | graphNEL | ✔ |
| pathview | Data integration and visualization on pathways | graphNEL | ✔ |
| KEGGgraph | Interface between KEGG pathways and graphs | graphNEL | ✔ |
| Gostats | Tools for interacting with Gene Ontology | graphNEL | ✔ |
| TCGAbiolinks | Integrative analysis with GDC data | igraph | ✔ |
| graphite | Graph objects from pathway databases | graphNEL | ✔ |
| minet | Infers mutual information networks | graphNEL | ✔ |
| SPIA | Signaling pathway impact analysis | graphNEL | ✔ |
| RDAVIDWebService | Retrieves data from DAVID | graphNEL | ✔ |
| STRINGdb | Retrieves interaction networks from STRING | igraph | ✔ |
| GENIE3 | Gene regulatory network inference | adjacency matrix | ✔ * |
| EnrichmentBrowser | Set and network-based enrichment analysis | graphNEL | ✔ |
| BioNet | Integrated network analysis and module detection | igraph, graphNEL | ✔ |
| GDCRNATools | Integrative analysis of lncRNA, mRNA and miRNA | dataframes | ✔ |
| CEMiTool | Analysis of coexpression gene modules | adjacency matrix | ✔ * |
| Linnorm | Linear model and normality based transformation | igraph | ✔ |
| RedeR | Interactive visualization of nested networks | igraph | ✔ |
| qpgraph | Estimate gene and eQTL networks | graphNEL | ✔ |
| RTN | Reconstruction of transcriptional networks | igraph | ✔ |
| rWikiPathways | Access WikiPathways web services | GPML | ✔ ** |
| hypergraph | Representing and manipulating hypergraphs | graphNEL | ✔ |
| apComplex | Bipartite graphs of complexes from AP-MS data | graphNEL | ✔ |
| cellTree | scRNA-seq data as a hierarchical tree structure | igraph | ✔ |
| FGNet | Functional gene networks from enrichment analyses | igraph | ✔ |
| SpidermiR | Integrative network analysis with miRNA data | igraph | ✔ |
| paxtoolsr | Access to BioPAX models in Pathway Commons | igraph, SIF | ✔ |
| netbiov | Visualization of large biological networks | igraph | ✔ |
| rsbml | Link to libsbml for SBML parsing | graphNEL | ✔ |
| ndexr | Interface to NDEx servers | igraph, CX | ✔ |