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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…

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…

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…

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…

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…

AMIGO2
Desktop

AMIGO2

A MATLAB environment to solve mathematical optimization problems which in…

A MATLAB environment to solve mathematical optimization problems which in dynamic modeling and control of biological systems. AMIGO2 is organized in four main modules: the pre-processor, the…

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
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…

optimusqual
Desktop

optimusqual

A Boolean regulatory network reconstruction using literature based knowledge.…

A Boolean regulatory network reconstruction using literature based knowledge. optimusqual has been implemented with a method which contextualized models from generic Prior knowledge networks (PKNs).…

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…

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…

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…

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…

PyBoolNet
Desktop

PyBoolNet

A Python package for the generation, modification and analysis of Boolean…

A Python package for the generation, modification and analysis of Boolean networks. The motivation for developing PyBoolNet was to offer a simple, well-documented interface to manipulating Boolean…

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…

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…

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…

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…

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…

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…

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…

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…

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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…

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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…

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…

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TBrowser
Desktop

TBrowser TranscriptomeBrowser

Hosts a large database of transcriptional signatures (TS, n~40 000) extracted…

Hosts a large database of transcriptional signatures (TS, n~40 000) extracted from Gene Expression Omnibus (~4 000 experiments) using the DBF-MCL algorithm. TBrowser constitutes a highly powerful…

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…

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 regulated, inhibited or activated in a biological system based on lists of upregulated and downregulated genes generated in microarray…

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DIANA-mirExTra
Web

DIANA-mirExTra

An online web server enabling users perform A-to-Z functional analyses,…

An online web server enabling users perform A-to-Z functional analyses, starting from next-generation sequencing expression data to the identification of important regulators with crucial roles in…

Integrity
Dataset

Integrity

Hosts a knowledgebase designed for drug discovery. The Integrity database…

Hosts a knowledgebase designed for drug discovery. The Integrity database contains a large collection of drugs which are annotated with information on their respective drug targets, the diseases they…

PRUNET
Desktop

PRUNET

A tool designed to address the contextualization of a prior knowledge gene…

A tool designed to address the contextualization of a prior knowledge gene regulatory networks (PKN) using a Booleanized representation of observed expression profiles corresponding to stable…

CARFMAP
Desktop

CARFMAP

An interactive cardiac fibroblast pathway map derived from the biomedical…

An interactive cardiac fibroblast pathway map derived from the biomedical literature using a software-assisted manual data collection approach. CARFMAP is an information-rich interactive tool that…

SINCERITIES
Desktop
BMALR
Desktop

BMALR Bayesian Model Averaging for Linear Regression

Reconstructs cellular regulatory networks. BMALR is a method to infer molecular…

Reconstructs cellular regulatory networks. BMALR is a method to infer molecular interactions in biological systems. The software uses a closed form solution to compute the posterior probabilities of…

DDGni
Desktop

DDGni Dynamic Delay Gene-network inference

A gene-network-inference algorithm based on the gapped local alignment of…

A gene-network-inference algorithm based on the gapped local alignment of gene-expression profiles. The local alignment can detect short-term gene regulations, that are usually overlooked by…

ASP-G
Desktop

ASP-G

A modular system to simulate Boolean network models of GRNs and to subsequently…

A modular system to simulate Boolean network models of GRNs and to subsequently compute their attractors. The main added value of ASP-G is in its modularity and declarativity, making it more flexible…

Cascade
Desktop

Cascade

Temporal gene interactions, in response to environmental stress, form a complex…

Temporal gene interactions, in response to environmental stress, form a complex system that can be efficiently described using gene regulatory networks. They allow highlighting the more influential…

BRANE Cut
Desktop

BRANE Cut Biologically-Related Apriori Network Enhancement with graph Cuts

A weighted graph thresholding method. Using biologically sound penalties and…

A weighted graph thresholding method. Using biologically sound penalties and data-driven parameters, BRANE Cut improves three state-of-the-art gene regulatory network (GRN) inference methods. The…

TimeDelay-ARACN…
Desktop

TimeDelay-ARACNE

An adaptation of the ARACNE algorithm to infer gene regulatory networks from…

An adaptation of the ARACNE algorithm to infer gene regulatory networks from time-course data, so that, the resulting network is represented as a directed graph. TimeDelay-ARACNE is expected to be…

minet
Desktop

minet Mutual Information NETworks

Provides a set of functions to infer mutual information networks from a…

Provides a set of functions to infer mutual information networks from a dataset. Once fed with a microarray dataset, the package returns a network where nodes denote genes, edges model statistical…

NetBenchmark
Desktop

NetBenchmark

Performs a systematic, yet fully reproducible, evaluation of transcriptional…

Performs a systematic, yet fully reproducible, evaluation of transcriptional network inference methods. NetBenchmark aggregates a large set of tools to assess the robustness of network inference…

ExTILAR
Desktop
cDREM
Desktop

cDREM Combinatorial Dynamic Regulatory Events Miner

A method for reconstructing dynamic models of combinatorial regulation. cDREM…

A method for reconstructing dynamic models of combinatorial regulation. cDREM integrates time series gene expression data with (static) protein interaction data. The method is based on a hidden…

MotifNetwork
Desktop

MotifNetwork

A program to analyze promoter motifs over Arabidopsis gene co-expression…

A program to analyze promoter motifs over Arabidopsis gene co-expression network. MotifNetwork uses a bottom-up approach to identify gene expression modules driven by known cis-regulatory motifs in…

LpRGNI
Desktop

LpRGNI Lp Regularization for Gene Network Inference

Infers gene regulatory networks with ChIP-seq data, transcriptome data and…

Infers gene regulatory networks with ChIP-seq data, transcriptome data and LASSO-type (Least absolute shrinkage and selection operator) regularization methods. LpRGNI applies two extended models of…

AtRegNet
Web

AtRegNet Arabidopsis thaliana Regulatory Network

Documents and visualizes networks formed by transcription factors (TFs) and…

Documents and visualizes networks formed by transcription factors (TFs) and their direct target genes only. AtRegNet visualizes regulatory networks and allows quick access and download of any…

NIMEFI
Desktop

NIMEFI Network Inference using Multiple Ensembles of Feature Importance algorithms

A general framework which casts any feature selection algorithm into an…

A general framework which casts any feature selection algorithm into an ensemble setting by taking random subsamples of varying size of both the experiments and the potential regulatory genes. NIMEFI…

ReNE
Desktop

ReNE

A Cytoscape application that enables a very quick enhancement of biological…

A Cytoscape application that enables a very quick enhancement of biological regulatory networks with additional transcriptional, post-transcriptional and translational information. Two main design…

Trigger
Desktop

Trigger

Allows statistical analysis of integrative genomic data. Trigger permits to…

Allows statistical analysis of integrative genomic data. Trigger permits to construct global linkage maps between genetic markers and gene expression. It can analyze multiple-locus linkage…

pathifier
Desktop

pathifier

Infers pathway deregulation scores for each tumor sample on the basis of…

Infers pathway deregulation scores for each tumor sample on the basis of expression data. Pathifier is an algorithm that transforms gene-level information into pathway-level information, generating a…

VTPNet
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VTPNet Variant-Transcription factor-Phenotype Networks

Uses as variant-transcription factor-phenotype networks. VTPNet defines tools…

Uses as variant-transcription factor-phenotype networks. VTPNet defines tools to investigate the construction and statistical interpretation of such bipartite graphs, which VTP (variant-transcription…

GPODE
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GPODE

Provides more accurate network structure learning. GPODE is a methodology for…

Provides more accurate network structure learning. GPODE is a methodology for the inference of GRNs from time-series and steady-state gene expression measurements. This framework is based on the use…

CyNetworkBMA
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CyNetworkBMA

A tool for inferring gene networks from expression data that integrates with…

A tool for inferring gene networks from expression data that integrates with Cytoscape. Our application offers a graphical user interface for networkBMA, an efficient implementation of Bayesian Model…

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miRTarVis
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