Bioconductor Packages

Affinity Network Fusion for Complex Patient Clustering

Batch Effects Quality Control Software

Model-View-Controller (MVC) Classes That Use Biobase

Biological Network Analysis in R

Biological Network Reconstruction Omnibus

Routines for the functional analysis of biological networks

CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks

Co-expression Modules identification Tool

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings

Causal network analysis methods

Calculate similarity of clusters from different single cell samples using foldchanges

Denoising Algorithm based on Relevance network Topology

Two-sample tests on a graph

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

Protein Interactions and Networks with Compounds based on Sequences using Deep Learning

Extending guilt by association by degree

Ensemble of Gene Set Enrichment Analyses

Seamless navigation through combined results of set-based and network-based enrichment analysis

Interpretation and enrichment for metabolomics data

GEne Network Inference with Ensemble of trees

Tools for manipulating GO and microarrays

Gene Regulatory Network Inference Using Time Series

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data

Gene set enrichment data structures and methods

Reproducible GSEA Benchmarking

Pipeline for augmented co-expression analysis

GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

Graph Theoretic Association Tests

GraphAlignment

A fast hierarchical graph-based clustering method

Interlog protein network reconstruction by Mapping and Mining ANalysis

Inference of gene regulatory networks from gene expression data

KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

Multi Omics Survival Clip

Model-View-Controller (MVC) Classes

MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

Pathways from the NCI Pathways Database

NetPathMiner for Biological Network Construction, Path Mining and Visualization

OmniPath web service client and more

Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

Phenotypes Identification Using Mapper from topological data Analysis

Inferring functionally related proteins using protein interaction networks

PathoStat Statistical Microbiome Analysis Package

Pedigree Functions

PhenoGeneRanker: A gene and phenotype prioritization tool