Bioconductor Packages

Infers biological signatures from gene expression data

Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

An interface to the BOOST graph library

Functions to Access and Control Cytoscape

Display and manipulate graphs in cytoscape.js

Convert a Graph into a D3js Script

Rapid Integration of Term Annotation and Network resources

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Analysis of co-regulation and inference of 'dual regulons'

Survival analysis using transcriptional networks inferred by the RTN package

Interactive visualization and manipulation of nested networks

Provides plotting capabilities for R graph objects

igraph library as an R package

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

SBML-R Interface and Analysis Tools

SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks

Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations

Sparse Inverse Covariance for Ecological Statistical Inference

Tools for Molecular Signatures

TRONCO, an R package for TRanslational ONCOlogy

Displaying binary trees with focus on dendrogram leaves

Comprehensive Visualization and Analysis of Multi-Set Intersections

Differential cell-type-specific allelic imbalance

Estimate protein complex membership using AP-MS protein data

Graph examples and use cases in Bioinformatics

Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

Differential gene co-expression

Differential co-expression/association network analysis

Diffusion scores on biological networks

Companion package to epiregulon with additional plotting, differential and graph functions

Hierarchical ensemble method based on factor graph

Tools for Manipulating the FOBI Ontology

Network Centrality Metrics for Elastic-Net Regularized Models

goProfiles: an R package for the statistical analysis of functional profiles

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

graph: A package to handle graph data structures

GRAPH Interaction from pathway Topological Environment

Gene Set Enrichment Analysis with Networks

HiPathia: High-throughput Pathway Analysis

Visualizing Hypergaphs

A package providing hypergraph data structures

Integrates DNA methylation data with gene expression in a single gene network

Interaction Based Homogeneity for Evaluating Gene Lists

Fast K-Nearest Neighbor Search for Single-Cell Analysis

graph support for KO, KEGG Orthology

Motif Analysis In Gene Regulatory Networks

GWAS Incorporating Networks

Mutual Information NETworks

Integrating microRNA expression into signaling pathways for pathway analysis