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Gene regulatory network inference software tools | Pathway analysis

Elucidating gene regulatory network (GRN) from large scale experimental data remains a central challenge in systems biology. The advent of high-throughput data generation technologies has allowed researchers to fit theoretical models to experimental…
CMGRN
Web

CMGRN Constructing Multilevel Gene Regulatory Networks

An integrative web server to unravel hierarchical interactive networks at…

An integrative web server to unravel hierarchical interactive networks at different regulatory levels. The developed method used the Bayesian network modeling to infer causal interrelationships among…

NIR
Desktop

NIR Network Inference by Reverse-engineering

Produces description of a network as a continuous time dynamical system. NIR…

Produces description of a network as a continuous time dynamical system. NIR can be applied to target prediction, and can be very useful for drug discovery. It uses measurements of mRNA concentration…

LibB
Desktop

LibB

Infers cellular networks. LibB is based on probabilistic graphical models that…

Infers cellular networks. LibB is based on probabilistic graphical models that represent multivariate joint probability distributions via a product of terms, each of which involves only a few…

BANJO
Desktop

BANJO BAyesian Network inference with Java Objects

Deciphers gene regulatory networks (GRNs) from gene expression data. BANJO…

Deciphers gene regulatory networks (GRNs) from gene expression data. BANJO permits users to infer putative information flow networks in the brain from microelectrode array data. It can handle…

rNAV
Desktop

rNAV rna NAVigator

Detects and filters bacterial sRNA targets for regulatory networks. rNAV is a…

Detects and filters bacterial sRNA targets for regulatory networks. rNAV is a visualization software designed to cope with a variety of biological constraints, including the gene annotations, the…

TSNI
Desktop

TSNI Time Series Network Identification

Allows users to recover direct targets of the transcription factor TRP63,…

Allows users to recover direct targets of the transcription factor TRP63, rather than the whole gene network. TSNI uses dynamic gene expression profiles to elucidate the function of a transcription…

DREM
Desktop

DREM Dynamic Regulatory Events Miner

Integrates static interaction data of dynamic regulatory networks with time…

Integrates static interaction data of dynamic regulatory networks with time series gene expression leading to models that can determine when transcription factors (TFs) activate genes and what genes…

C3NET
Desktop

C3NET C3NET

Allows inferring gene regulatory networks with direct physical interactions…

Allows inferring gene regulatory networks with direct physical interactions from microarray expression data. For systems biology to succeed in the long run, it is of crucial importance to establish…

MERLIN
Desktop

MERLIN Modular regulatory network learning with per gene information

Infers regulatory programs for individual genes while probabilistically…

Infers regulatory programs for individual genes while probabilistically constraining these programs to reveal module-level organization of regulatory networks. MERLIN is an algorithm for learning…

Ometer
Desktop

Ometer

Constructs approximate undirected dependency graphs (UDGs) from large-scale…

Constructs approximate undirected dependency graphs (UDGs) from large-scale biochemical data. Ometer uses partial correlation coefficients to proceed. It is able to efficiently analyze genome-sized…

CRCmapper
Desktop

CRCmapper Core Regulatory Circuitries mapper

Identifies core regulatory circuitry using as input H3K27ac ChIP-seq reads…

Identifies core regulatory circuitry using as input H3K27ac ChIP-seq reads aligned to the human genome, together with the ChIP-seq peaks identified by Magnetic-Activated Cell Sorting (MACS) and the…

GAGE
Desktop

GAGE Generally Applicable Gene-set Enrichment

Allows gene set or pathway analysis. GAGE is able to reveal novel and relevant…

Allows gene set or pathway analysis. GAGE is able to reveal novel and relevant regulatory mechanisms from microarray studies. It produces good results concerning consistency across parallel studies…

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VCNet
Desktop

VCNet

Constructs gene co-expression network (GCN) from RNA-seq data. VCNet performs a…

Constructs gene co-expression network (GCN) from RNA-seq data. VCNet performs a statistical hypothesis test based on the correlation matrix of a gene-gene pair using the Frobenius norm. It can detect…

GeNeDA
Web

GeNeDA Gene Regulatory Network Design Automation

Provides open-source tools dedicated to design automation of artificial gene…

Provides open-source tools dedicated to design automation of artificial gene regulatory networks (GRNs) based on a digital approach. GeNeDA is a framework composed of six parts: (i) the input…

ARACNE
Desktop

ARACNE Algorithm for the Reconstruction of Accurate Cellular Networks

An algorithm, using microarray expression profiles, specifically designed to…

An algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of…

SpidermiR
Desktop

SpidermiR

Offers an easy access to both Gene Regulatory Networks (GRNs) and miRNAs to the…

Offers an easy access to both Gene Regulatory Networks (GRNs) and miRNAs to the end user. SpidermiR integrates co-expression, physical interaction, co-localization, genetic influence, pathways, and…

ARACNe-AP
Desktop
biRte
Desktop

biRte

A computationally attractive approach combining Bayesian inference of regulator…

A computationally attractive approach combining Bayesian inference of regulator activities with network reverse engineering. biRte integrates target gene predictions with different omics data…

SMITE
Desktop

SMITE Significance-based Modules Integrating the Transcriptome and Epigenome

Integrates transcriptional and epigenetic regulatory data without loss of…

Integrates transcriptional and epigenetic regulatory data without loss of resolution. SMITE combines p-values by accounting for the correlation between non-independent values within data sets,…

GENIE3
Desktop

GENIE3

An algorithm for the inference of gene regulatory networks from expression…

An algorithm for the inference of gene regulatory networks from expression data. It decomposes the prediction of a regulatory network between p genes into p different regression problems. In each of…

LDGM
Desktop

LDGM Latent Differential Graphical Model

A method to infer differential network among different tissues. LDGM method…

A method to infer differential network among different tissues. LDGM method allows to estimate the differential network between two tissue types directly, without inferring the network for individual…

MIPRIP
Desktop

MIPRIP Mixed Integer linear Programming based Regulatory Interaction Predictor

Predicts regulators of a gene of interest from gene expression profiles of the…

Predicts regulators of a gene of interest from gene expression profiles of the samples under study and known regulator binding information (from e.g. ChIP-seq/ChIP-chip databases). MIPRIP is…

ChIP-Array
Web

ChIP-Array

A web-based tool integrating transcription factor (TF) binding and…

A web-based tool integrating transcription factor (TF) binding and transcriptome data to construct a gene regulatory network controlled by a transcription factor. ChIP-Array assists biologists to…

NLNET
Desktop
HTS-Net
Web
Desktop

HTS-Net High-Throughput screening - Network analysis

Provides a method for RNAi screenings network analyses. HTS-Net intends to…

Provides a method for RNAi screenings network analyses. HTS-Net intends to improve the Interactome-Transcriptome Integration (ITI) algorithm. The pipeline aims to optimize the subnetworks detection…

GRNBoost
Desktop

GRNBoost

Infers regulators for each target gene purely from a gene expression matrix.…

Infers regulators for each target gene purely from a gene expression matrix. GRNBoost uses gradient boosted stumps as the base learner. It will permit network inference on very large data sets. The…

RGBM
Desktop

RGBM Regularized Gradient Boosting Machines

Supplies an implementation of Regularized LS-TreeBoost & LAD-TreeBoost…

Supplies an implementation of Regularized LS-TreeBoost & LAD-TreeBoost algorithm for Regulatory Network inference from any type of expression data. RGBM is a gene regulatory network (GRN)…

NetLand
Desktop

NetLand

Models and simulates the kinetic dynamics of gene regulatory networks (GRNs).…

Models and simulates the kinetic dynamics of gene regulatory networks (GRNs). NetLand allows to visualize the corresponding Waddington’s epigenetic landscape in three dimensions without restriction…

TheCellMap.org
Web

TheCellMap.org

Allows to explore the extent to which genetic interactions reveal cellular…

Allows to explore the extent to which genetic interactions reveal cellular function and contribute to complex phenotypes for Saccharomyces cerevisiae. TheCellMap.org emphasizes the prevalence of…

RTNduals
Desktop

RTNduals

Searches for possible co-regulatory loops between regulon pairs generated by…

Searches for possible co-regulatory loops between regulon pairs generated by the RTN (Reconstruction of Transcriptional Networks) package. RTNduals searches for targets shared between pairs of…

APA
Desktop

APA Altered Pathway Analyzer

Identifies and prioritizes altered pathways, including those which are…

Identifies and prioritizes altered pathways, including those which are differentially regulated by transcription factors (TFs), by quantifying rewired sub-network topology. Altered Pathway Analyzer…

MBTPROM
Desktop

MBTPROM Mycobacterium tuberculosis Probabilistic Regulation of Metabolism

Encapsulates a substantially expanded knowledge base of underlying metabolic…

Encapsulates a substantially expanded knowledge base of underlying metabolic and regulatory mechanisms. MTBPROM2.0 is a model that can predict metabolic consequences of transcription factor (TF)…

COREGNET
Desktop

COREGNET

An R/Bioconductor package to analyze large-scale transcriptomic data by…

An R/Bioconductor package to analyze large-scale transcriptomic data by highlighting sets of co-regulators. Based on a transcriptomic dataset, COREGNET can be used to: reconstruct a large-scale…

CABERNET
Desktop
PANDA
Desktop

PANDA Passing Attributes between Networks for Data Assimilation

Models information flow in regulatory networks using an integrative approach.…

Models information flow in regulatory networks using an integrative approach. PANDA is a message-passing model which searches for agreement among various data-types using information from each to…

PhenoProphet
Desktop

PhenoProphet

Assigns each transcription factor (TF) in a network a score representing the…

Assigns each transcription factor (TF) in a network a score representing the confidence that the deletion of that TF will yield a phenotypic change of interest. The PhenoProphet score of a TF for a…

Inferelator
Desktop

Inferelator

Genetic regulatory networks inference algorithm. Key developments included:…

Genetic regulatory networks inference algorithm. Key developments included: modeling of environment and TF interactions, the use of a model fitting procedure that allows for missing data and…

TILAR
Desktop

TILAR Transcription Factor binding site integrating Least Angle RegreSsion

Allows deduction of gene regulatory interactions from gene expression data by…

Allows deduction of gene regulatory interactions from gene expression data by integrating information on transcription factor binding sites (TFBS). TILAR has been developed to reconstruct…

Parmigene
Desktop

Parmigene PARallel Mutual Information estimation for GEne NEtwork reconstruction

Provides a parallel estimation of the mutual information based on entropy…

Provides a parallel estimation of the mutual information based on entropy estimates from k-nearest neighbor (KNN) distances and algorithms for the reconstruction of gene regulatory networks.…

Sets2Networks
Web
Desktop

Sets2Networks

Converts any entity-set library into a network. Sets2Networks is a general…

Converts any entity-set library into a network. Sets2Networks is a general method for network inference from repeated observations of sets of related entities. The synthetic network is first…

CellBranch
Desktop

CellBranch

Aims to capture and integrate the results of multiple high-throughput…

Aims to capture and integrate the results of multiple high-throughput experiments. CellBranch allows users to model protein expression, particularly transcription factor (TF) expression, across…

icTAIR
Desktop

icTAIR iterative Contextual Transcriptional Activity Inference of Regulators

Contextually-refines regulator target gene lists. icTAIR takes a regulator’s…

Contextually-refines regulator target gene lists. icTAIR takes a regulator’s previously-identified target gene list and combines it with gene expression data from a context, quantifying that…

MarA Multigene…
Desktop

MarA Multigene Regulation

Regulates small RNAs, metabolic enzymes, efflux pumps, and regulatory proteins.…

Regulates small RNAs, metabolic enzymes, efflux pumps, and regulatory proteins. MarA Multigene Regulation regulates over 60 downstream targets by binding to a well-characterized degenerate binding…

FastNCA
Desktop

FastNCA Fast Network Component Analysis

Reconstructs gene regulatory network (GRN) from microarray data. FastNCA was…

Reconstructs gene regulatory network (GRN) from microarray data. FastNCA was tested on a sample of 100 Monte Carlo experiments. It returns a mean almost equal to the median of the fitting error. This…

SynTReN
Desktop

SynTReN Synthetic Transcriptional Regulatory Networks

Produces simulated gene expression data which approximates experimental data,…

Produces simulated gene expression data which approximates experimental data, creates synthetic transcriptional regulatory networks and corresponding microarray data sets. SynTReN is a generator of…

netClass
Desktop

netClass

An R package for network-based feature (gene) selection for biomarkers…

An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. This package adapts the following 5 algorithms for classifying and predicting…

PMN
Desktop

PMN Physical Module Networks

Learns transcriptional networks by combining phenotypic effects (changes in…

Learns transcriptional networks by combining phenotypic effects (changes in gene expression) with their underlying physical mechanism (protein–protein and protein–DNA interactions). PMN is a…

TIGRESS
Desktop

TIGRESS Trustful Inference of Gene REgulation using Stability Selection

A scoring technique for stability selection, which improves the performance of…

A scoring technique for stability selection, which improves the performance of feature selection with LARS. TIGRESS reaches state-of-the-art performance on benchmark data, including both in silico…

predictionet
Desktop

predictionet

Contains a set of functions related to network inference combining genomic data…

Contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases. The main function is…

TFmiR
Web

TFmiR

A freely available web server for deep and integrative analysis of…

A freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease…

CL
Web

CL Cancer Landscapes

Provides data-derived statistical network models for 8 human cancers. CL…

Provides data-derived statistical network models for 8 human cancers. CL contains several functions for biological interpretability of the network models, such as pathway analysis, drug-target…

qpgraph
Desktop

qpgraph

Estimates gene and eQTL networks from high-throughput expression and genotyping…

Estimates gene and eQTL networks from high-throughput expression and genotyping assays. qpgraph is based in the so-called q-order limited partial correlation graphs, qp-graphs, which is specifically…

F-MAP
Desktop

F-MAP

Reconstructs gene regulatory network by using the external knowledge about gene…

Reconstructs gene regulatory network by using the external knowledge about gene interactions drawn from the other related species gene expressions data. F-MAP is a combination of factor analysis and…

GeneReg
Desktop

GeneReg

Constructs gene regulatory network (GRN) from short time course gene expression…

Constructs gene regulatory network (GRN) from short time course gene expression data. GeneReg is based on a time delay linear regression model. It implements a linear function with two parameters,…

GeNGe
Web

GeNGe GEne Network GEnerator

Allows to model gene regulatory networks (GRNs) of different types. GeNGe uses…

Allows to model gene regulatory networks (GRNs) of different types. GeNGe uses GRNs in order to set up a deterministic ordinary differential equation (ODE) system. It offers features for the…

SeqSpider
Desktop

SeqSpider

Enables learning from tag distributions, a unique feature of ChIP-Seq and…

Enables learning from tag distributions, a unique feature of ChIP-Seq and bisulfite sequencing data, and combined with a profile clustering method for noise removal. SeqSpider is a Bayesian network…

TRFBA
Desktop

TRFBA Transcriptional Regulated Flux Balance Analysis

Uses all the gene expression data for various genetic or environmental…

Uses all the gene expression data for various genetic or environmental perturbations and introduces constraints to convert gene expression levels to the upper bounds of reactions. The proposed…

PyPanda
Desktop

PyPanda

A gene regulatory network inference method that uses message-passing to…

A gene regulatory network inference method that uses message-passing to integrate multiple sources of ‘omics data. PANDA was originally coded in C++. PyPanda is the Python version of PANDA. PyPanda…

LEM
Algorithm

LEM Latent effect mechanistic

A mechanistic analysis method that can be used to detect and analyze latent…

A mechanistic analysis method that can be used to detect and analyze latent processes which affect the molecular mechanisms by rewiring the underlying network structure. LEM model is based on the…

REDUCE
Desktop

REDUCE REDuction of UnCertain Edges

An algorithm for optimal design of gene knock-out (KO) for the purpose of gene…

An algorithm for optimal design of gene knock-out (KO) for the purpose of gene regulatory network (GRN) inference. REDUCE employed ensemble inference to define uncertain gene interactions that could…

Moksiskaan
Desktop

Moksiskaan

A computational platform that can be used to integrate information about the…

A computational platform that can be used to integrate information about the connections between genes, proteins, pathways, drugs, and other biological entities. The database is used to combine…

sgnesR
Desktop

sgnesR Stochastic Gene Network Expression Simulator in R

Utilizes the applicability of gene expression simulations. sgnesR is an…

Utilizes the applicability of gene expression simulations. sgnesR is an easy-to-use interface for the simulation of gene expression profiles from a given network structure. Researchers can use a…

CMI2NI
Desktop

CMI2NI

Permits to infer gene regulatory networks (GRNs) of gene expression data. The…

Permits to infer gene regulatory networks (GRNs) of gene expression data. The CMI2NI method uses a concept of Conditional Mutual Inclusive Information (CMI2) measuring direct dependences between…

PCA-CMI
Desktop

PCA-CMI PC-Algorithm Based on Conditional Mutual Information

Allows to infer gene regulatory networks (GRNs) from gene expression data. The…

Allows to infer gene regulatory networks (GRNs) from gene expression data. The PCA-CMI method is based on conditional mutual information considering the non-linear dependence and topological…

DMI
Desktop

DMI Decomposable Multi-structure Identification

Identifies genome-wide gene regulatory network (GRN) structures. The GRN…

Identifies genome-wide gene regulatory network (GRN) structures. The GRN structure identified by the DMI algorithm could reveal possible biological links and help researchers to choose which gene…

EMBN
Desktop

EMBN Epigenetic Module based on Differential Networks

Prevents the specification of the correlation between methylation and…

Prevents the specification of the correlation between methylation and expression. EMBN is a multiple network framework for epigenetic modules that can recognize positively and negatively correlated…

CGC-2SPR
Desktop

CGC-2SPR CGC using two-step prior Ridge regularization

A method that can effectively incorporate prior knowledge into Granger…

A method that can effectively incorporate prior knowledge into Granger causality analysis, and accurately derive causal relations between gene pairs from gene expression time series data. In our…

GEPASI
Desktop

GEPASI GEneral PAthway Simulator

Allows users to model dynamics, steady states and control of biochemical or…

Allows users to model dynamics, steady states and control of biochemical or other systems. GEPASI has a modular structure that makes possible the existence of several user interfaces, the numerical…

GEMULA
Desktop

GEMULA

Identifies context-specific gene regulatory networks based on linear models and…

Identifies context-specific gene regulatory networks based on linear models and parameter estimation using lasso. GEMULA is a software, based on linear models, which can identify context-specific…

MotifMap
Web

MotifMap

Provides comprehensive maps of candidate regulatory elements encoded in the…

Provides comprehensive maps of candidate regulatory elements encoded in the genomes of model species. Motifmap allows to select a transcription factor (TF), view its binding sequence logo, and list…

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miRLAB
Desktop

miRLAB

Automates the procedure of inferring and validating miRNA-mRNA regulatory…

Automates the procedure of inferring and validating miRNA-mRNA regulatory relationships. miRLAB provides a complete set of pipelines for testing new methods and analysing new datasets. It includes a…

SYGNAL
Desktop

SYGNAL SYstems Genetic Network AnaLysis

Infers the causal flow of information from mutations to regulators to perturbed…

Infers the causal flow of information from mutations to regulators to perturbed gene expression patterns across patient tumors. SYGNAL integrates a method for constructing a mechanistic transcription…

HRNN
Desktop

HRNN Hierarchical Recurrent Neural Network

Identifies time-delayed regulatory interactions of genes. HRNN is a method that…

Identifies time-delayed regulatory interactions of genes. HRNN is a method that surmounts the interpretation difficulties of recurrent neural network (RNN) for application of gene regulatory networks…

iRegulon
Desktop

iRegulon

A regulon consists of a transcription factor (TF) and its direct…

A regulon consists of a transcription factor (TF) and its direct transcriptional targets, which contain common TF binding sites in their cis-regulatory control elements. The iRegulon plugin allows…

GeNICE
Desktop
Beacon GRN…
Desktop

Beacon GRN inference

Predicts gene regulatory networks (GRNs) occurring during seed development in…

Predicts gene regulatory networks (GRNs) occurring during seed development in Arabidopsis based on a support vector machine (SVM) model. Beacon GRN inference provides a valuable model system for…

ReconstructionG…
Desktop

ReconstructionGRNfromGeneticalGenomicsData

Reconstructs gene regulatory networks (GRNs) from genetical genomics data.…

Reconstructs gene regulatory networks (GRNs) from genetical genomics data. ReconstructionGRNfromGeneticalGenomicsData was applied to synthetic genetical genomics data that were provided for a recent…

RENCO
Desktop

RENCO REgulatory Network generator with COmbinatorial control

Automatically generates differential equations describing pre-transcriptional…

Automatically generates differential equations describing pre-transcriptional combinatorics in artificial regulatory networks. RENCO is a software which models genes and proteins as separate…

DRYGIN
Dataset

DRYGIN Data Repository of Yeast Genetic Interactions

Aims at providing a central platform for yeast genetic network analysis and…

Aims at providing a central platform for yeast genetic network analysis and visualization. DRYGIN holds more than 5.4 million measurements of genetic interacting pairs involving 4500 genes. It…

ARTIVA
Desktop

ARTIVA Auto Regressive TIme VArying regulatory models

A statistical framework to infer time-varying structures of gene-regulation…

A statistical framework to infer time-varying structures of gene-regulation networks. ARTIVA performs an analysis of time-course gene expression measurements (for instance transcriptional data) to…

Operator-valued…
Desktop

Operator-valued Kernel-based Vector AutoRegressive-Boost

Shares features from L2-boosting. OKVAR-Boost shares features with boosting and…

Shares features from L2-boosting. OKVAR-Boost shares features with boosting and selected features of randomization-based methods, such as the use of a random subnetwork at each iteration. It exhibits…

JCell
Desktop

JCell

Provides several algorithms to identify genetic and metabolic dependencies…

Provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. JCell is a…

G T A T C G C T A
Magia
Web

Magia

A web application for the integrative analysis of in silico target prediction,…

A web application for the integrative analysis of in silico target prediction, miRNA and gene expression data. MAGIA2 refines in silico target prediction through miRNA–target expression association…

G T A T C G C T A
PTHGRN
Web

PTHGRN Post-Translational Hierarchical Gene Regulatory Network

An open web server to unravel relationships among PTMs, TFs, epigenetic…

An open web server to unravel relationships among PTMs, TFs, epigenetic modifications and gene expression. PTHGRN accepts three input: PPI, ChIP-seq binding peaks of TFs and epigenetic modifications,…

LoTo
Web

LoTo Local Topological comparison of directed networks

Implements both graphlets metrics REC (REConstruction Rate) and RGD (REC…

Implements both graphlets metrics REC (REConstruction Rate) and RGD (REC Graphlet Degree) to conduct differential analyses of gene regulatory network. LoTo compares the occurrence of graphlets in a…

MIDER
Desktop

MIDER Mutual Information Distance and Entropy Reduction

A general purpose software tool for inferring network structures. MIDER…

A general purpose software tool for inferring network structures. MIDER provides a representation of the network in which the distance among nodes indicates their statistical closeness. It refines…

AR1MA1-VBEM
Desktop

AR1MA1-VBEM

Provides a variation of Bayesian framework. AR1MA1-VBEM compiles scripts to…

Provides a variation of Bayesian framework. AR1MA1-VBEM compiles scripts to perform Gene Regulatory Network (GRN) inference from time series or pseudo-time series data using a first-order…

FANOVA
Desktop

FANOVA Functional ANalysis Of VAriance

Allows discovery of unknown gene functions. FANOVA is based on a Gaussian…

Allows discovery of unknown gene functions. FANOVA is based on a Gaussian process. It can identify significant differential growth between the trajectories of transcription factor (TF) knockouts…

SITAR
Desktop

SITAR Sparse latent varIable model of TrAnscritional Regulation

Makes quantitative inferences of regulatory networks, including binary…

Makes quantitative inferences of regulatory networks, including binary transcription factors (TFs)-gene interactions as well as latent activities of TFs. SITAR is a Bayesian sparse factor analysis…

MotifNet
Web

MotifNet

Provides an open-access web-server for network motif analysis. MotifNet…

Provides an open-access web-server for network motif analysis. MotifNet functions as an interactive browser for exploring the motifs and their instances. The user can filter motifs by their…

G T A T C G C T A
SCENIC
Desktop

SCENIC Single Cell rEgulatory Network Inference and Clustering

Allows to reconstruct gene regulatory networks (GRNs). SCENIC uses single-cell…

Allows to reconstruct gene regulatory networks (GRNs). SCENIC uses single-cell RNA-seq data to identify stable cell states. It analyzes all the co-expression modules using cis-regulatory motif…

NetMiner
Desktop

NetMiner

Allows to build a high-quality RNA-seq-based Gene Co-expression Network (GCN)…

Allows to build a high-quality RNA-seq-based Gene Co-expression Network (GCN) in rice. NetMiner is based on the hypothesis that the different network inference methods have complementary advantages…

BRANE Clust
Desktop

BRANE Clust

Refines gene regulatory network (GRN) inference thanks to cluster information.…

Refines gene regulatory network (GRN) inference thanks to cluster information. BRANE Clust works as a post-processing tool for inference methods. The clustering is based on the inversion of a system…

LASSIM
Desktop

LASSIM LArge-Scale SImulation Modeling

Performs large-scale inference using mechanistically defined ordinary…

Performs large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory…

fastBMA
Desktop

fastBMA

A distributed, parallel and scalable implementation of Bayesian model averaging…

A distributed, parallel and scalable implementation of Bayesian model averaging for this purpose. fastBMA includes a novel and computationally efficient method for eliminating redundant indirect…

SIMoNe
Desktop

SIMoNe Statistical Inference for MOdular NEtworks

Enables inference of gene-regulatory networks based on partial correlation…

Enables inference of gene-regulatory networks based on partial correlation coefficients from microarray experiments. SIMoNe is based on a Gaussian graphical model and estimates non-zero entries of…

PCIT
Desktop

PCIT Partial Correlation coefficient with Information Theory

Detects meaningful gene–gene associations in co-expression networks. PCIT…

Detects meaningful gene–gene associations in co-expression networks. PCIT provides a flexible means for applying the PCIT algorithm to gene co-expression networks (GCN), and also allows this to be…

GeStoDifferent
Desktop

GeStoDifferent

Aims at the generation and the identification of gene regulatory networks…

Aims at the generation and the identification of gene regulatory networks (GRNs) describing an arbitrary stochastic cell differentiation process. The (dynamical) model adopted to describe general…

inferenceSnapsh…
Desktop

inferenceSnapshot

Allows to recover the temporal behaviour from single-cell snapshot data and…

Allows to recover the temporal behaviour from single-cell snapshot data and reverse engineer the dynamics of gene expression. The framework combines a dimensionality reduction method with a cell…

iRafNet
Desktop

iRafNet

A flexible, unified integrative framework that allows information from…

A flexible, unified integrative framework that allows information from heterogeneous data, such as protein-protein interactions, transcription factor (TF)-DNA-binding, gene knock-down, to be jointly…

CoMoFinder
Desktop

CoMoFinder

Strives to discover reliable composite network motifs in co-regulatory networks…

Strives to discover reliable composite network motifs in co-regulatory networks which consist of microRNAs, transcriptional regulators and genes.

inferenceNetwor…
Desktop

inferenceNetwork

A multi-layer graphical model that is capable of leveraging many publicly…

A multi-layer graphical model that is capable of leveraging many publicly available time-course datasets, as well as a cell lineage-specific data with small sample size, to model regulatory networks…

GeNOSA
Desktop

GeNOSA

The establishment of quantitative gene regulatory networks (qGRNs) through…

The establishment of quantitative gene regulatory networks (qGRNs) through existing network component analysis (NCA) approaches suffers from shortcomings such as usage limitations of problem…

jump3
Desktop

jump3

A hybrid approach for GRN inference exploiting time series of expression data.…

A hybrid approach for GRN inference exploiting time series of expression data. Jump3 is based on a formal on/off model of gene expression but uses a non-parametric procedure based on decision trees…

SMARTS
Desktop

SMARTS Scalable Models for the Analysis of Regulation from Time Series

A method integrating static and time series data from multiple individuals to…

A method integrating static and time series data from multiple individuals to reconstruct condition-specific response networks in an unsupervised way. Using probabilistic graphical models, SMARTS…

PLSNET
Desktop

PLSNET

An ensemble gene regulatory network inference method. PLSNET decomposes the…

An ensemble gene regulatory network inference method. PLSNET decomposes the gene regulatory network (GRN) inference problem with p genes into p subproblems and solves each of the subproblems by using…

Jimena
Desktop

Jimena

A Java genetic regulatory network simulation framework which focuses on…

A Java genetic regulatory network simulation framework which focuses on computational efficacy and a modularized architecture to facilitate the development and testing of new algorithms and models…

NetProphet
Desktop

NetProphet

An algorithm for inferring transcriptional regulatory networks from gene…

An algorithm for inferring transcriptional regulatory networks from gene expression data. NetProphet capitalizes on the complementarity of the coexpression and differential expression (DE) strategies…

HumanNet
Dataset

HumanNet Human gene functional interaction Network

A probabilistic functional gene network of 18,714 validated protein-encoding…

A probabilistic functional gene network of 18,714 validated protein-encoding genes of Homo sapiens, constructed by a modified Bayesian integration of 21 types of 'omics' data from multiple…

CroCo
Web
Desktop

CroCo Cross-species Conservation

Provides a network-oriented view on the ENCODE regulatory data (CroCo network…

Provides a network-oriented view on the ENCODE regulatory data (CroCo network repository), convenient ways to access and browse networks and metadata, and a method to combine networks across…

LegumeGRN
Web

LegumeGRN

Builds, analyzes and visualizes gene regulatory networks (GRNs) that govern…

Builds, analyzes and visualizes gene regulatory networks (GRNs) that govern various biological processes. LegumeGRN is a web-based developed to help biologists to investigate gene regulatory…

Loregic
Desktop

Loregic

A multi-purpose computational method that uses logic-circuit models to…

A multi-purpose computational method that uses logic-circuit models to characterize the cooperativity among regulatory factors such as TFs and miRNAs by integrating gene expression and regulatory…

PathWave
Desktop

PathWave

Enables the identification of disease specific regulation patterns by combining…

Enables the identification of disease specific regulation patterns by combining gene expression data and network topology. PathWave is preferable to classical enrichment tests as it offers a much…

ModEnt
Desktop

ModEnt

A computational tool that reconstructs gene regulatory networks from high…

A computational tool that reconstructs gene regulatory networks from high throughput experimental data. ModEnt is a probabilistic formulation of the problem that circumvents discretization of…

AtPAN
Web

AtPAN Arabidopsis thaliana Promoter Analysis Net

Detects transcription factor binding sites (TFBSs) and their corresponding…

Detects transcription factor binding sites (TFBSs) and their corresponding transcription factors (TFs) in a promoter or a set of promoters in Arabidopsis. AtPAN provides a comparative analysis…

NetSim
Desktop

NetSim

Represents a gene network simulator. The NetSim simulator generates network…

Represents a gene network simulator. The NetSim simulator generates network topology according to the current knowledge of biological network organization. This includes clustering coefficient…

mirConnX
Web

mirConnX

A user-friendly web interface for inferring, displaying and parsing mRNA and…

A user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to…

MMIA
Web

MMIA miRNA-mRNA Integrated Analysis

Integrates microRNA and mRNA expression data with predicted microRNA target…

Integrates microRNA and mRNA expression data with predicted microRNA target information for analyzing microRNA-associated phenotypes and biological functions by gene set enrichment analysis (GSEA).…

TFactS
Web

TFactS

A tool designed to predict which transcription factors are regulated, inhibited…

A tool designed to predict which transcription factors are re