Bioconductor Packages

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Biological Network Reconstruction Omnibus

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

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

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

Integration of CellNOptR to add missing links

Epistasis Analysis for Quantitative Traits by Functional Regression Model

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

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

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

Host-Pathogen Interaction Prediction

R implementation of information measures

Inference of gene regulatory networks from gene expression data

Visualize all edges within a KEGG pathway and overlay LINCS data

Integrate microRNA and gene expression to decipher pathway complexity

Multi Omic Master Regulator Analysis

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

Prediction of pathway-related protein-protein interaction networks

PhenoGeneRanker: A gene and phenotype prioritization tool

Infers biological signatures from gene expression data

Predicting Interactomes from Co-Elution

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

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

Gene regulator enrichment analysis

S-system parameter estimation method

Sparse Partial Correlations On Gene Expression

Cell Signalling Using Single-Cell RNA-seq or Proteomics Data

Sparse Inverse Covariance for Ecological Statistical Inference

TRONCO, an R package for TRanslational ONCOlogy

Estimate protein complex membership using AP-MS protein data

Training of logical models from indirect measurements of perturbation experiments

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

Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

Differential co-expression/association network analysis

epiNEM

Hierarchical ensemble method based on factor graph

Synthetic Expression Data for Gene Regulatory Network Inference

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

Modeling networks for individual samples using LIONESS

Linear Programming Model for Network Inference

Dry lab for exploring miRNA-mRNA relationships

Mutual Information NETworks

Mixture Nested Effects Models