Bioconductor Packages

Adaptive Dropout Imputer (ADImpute)

Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

Affinity Network Fusion for Complex Patient Clustering

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

Functional Similarities

Biological Network Analysis in R

Biological Network Reconstruction Omnibus

Routines for the functional analysis of biological networks

Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

plot bayesian network inferred from gene expression data based on enrichment analysis results

Plots For Visualising Cell-Cell Interactions

Co-expression Modules identification Tool

Addon to CellNOptR: Fuzzy Logic

Package for CTDbase data query, visualization and downstream analysis

Causal network analysis methods

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Two-sample tests on a graph

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

Differential Network Enrichment Analysis for Biological Data

DeMAND

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

Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer

Extending guilt by association by degree

Ensemble of Gene Set Enrichment Analyses

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

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

Exposure-Aware Multi-Omics Risk Modeling

Interpretation and enrichment for metabolomics data

Functional Gene Networks derived from biological enrichment analyses

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

GEne Network Inference with Ensemble of trees

Constructing gene regulatory networks from expression data through functional module inference

GO-terms Semantic Similarity Measures

Gene Regulatory Network Inference Using Time Series

Reproducible GSEA Benchmarking

Pipeline for augmented co-expression analysis

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

Graph Theoretic Association Tests

GraphAlignment

S4 Class for Quantitative Data and Associated Networks

Host-Pathogen Interaction Prediction

Interlog protein network reconstruction by Mapping and Mining ANalysis

R implementation of information measures

Inference of gene regulatory networks from gene expression data

KinSwingR: network-based kinase activity prediction

Linear model and normality based normalization and transformation method (Linnorm)

LiquidAssociation