Biocview "NetworkInference"

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

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

analysis of co-regulatory network motifs and inference of 'dual regulons'.

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

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

A Toolkit for Flow And Mass Cytometry Data

Bayesian Inference of Regulatory Influence on Expression (biRte)

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Benchmarking of several gene network inference methods

Biological Network Analysis

Biological Network Reconstruction Omnibus

ceRNAR: An R Package for Identification and Analysis of ceRNAs-miRNA Triplets

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

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

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

Constructing gene regulatory networks from expression data through functional module inference

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

Differential co-expression/association network analysis

Differentially Expressed Gene-Gene pairs

Dry lab for exploring miRNA-mRNA relationships

(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

epiNEM

Epistasis Analysis for Quantitative Traits by Functional Regression Model

Estimate protein complex membership using AP-MS protein data

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Fit transcriptional regulatory networks using gene expression, priors, machine learning

Functional Network Analysis

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

GEne Network Inference with Ensemble of trees

Gene regulator enrichment analysis

Gene Regulatory Network Inference Using Time Series

Genetic inteRaction and EssenTiality neTwork mApper

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

Hidden Variable Dynamic Modeling

Hierarchical ensemble method based on factor graph

Host-Pathogen Interaction Prediction

Identifying genetic trait/phenotype relevant cell type/state at single cell resolution

Inference And Analysis Of Synteny Networks

Inference for predictive networks designed for (but not limited to) genomic data

Inference of gene regulatory networks from gene expression data

Inferring unobserved perturbations from gene expression data

Infers biological signatures from gene expression data

In Silico Interactome

Integration of CellNOptR to add missing links

JODA algorithm for quantifying gene deregulation using knowledge

Linear Programming Model for Network Inference

Mixture Nested Effects Models

Modeling networks for individual samples using LIONESS

Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Multi Omic Master Regulator Analysis

Multi-omics Classification, Functional Enrichment and Network Inference analysis

Multi-Omics (time-course) network-based integration and interpretation

Mutual Information NETworks

PANDA Algorithm

PhenoGeneRanker: A gene and phenotype prioritization tool

Phenotype-driven module identification

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

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

Predicting Interactomes from Co-Elution

Prediction of pathway-related protein-protein interaction networks

Probabilistic combinatorial nested effects model

Protein-Protein Interaction Statistical Package

Random walk with restart on multiplex and heterogeneous Networks

Rapid Integration of Term Annotation and Network resources

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

Regression-based network inference using Bayesian Model Averaging

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

regutools: an R package for data extraction from RegulonDB

R implementation of Information measures

R implementation of informtion measures

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Single Cell Inference of Regulatory Activity

Sparse Partial Correlations On Gene Expression

Spatial quantile normalization

S-system parameter estimation method

Survival analysis using transcriptional networks inferred by the RTN package

Synthetic Expression Data for Gene Regulatory Network Inference

Systems EPigenomics Inference of Regulatory Activity

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Training of logical models from indirect measurements of perturbation experiments

Transcriptional Data Guided fMRI Network Classification

Transcription factor Inference through Gaussian process Reconstruction of Expression

TRONCO, an R package for TRanslational ONCOlogy

Unified methods for the inference and analysis of gene regulatory networks

Visualize all edges within a KEGG pathway and overlay LINCS data

Visualize all edges within a KEGG pathway and overlay LINCS data [option]

Biocview "NetworkInference"

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