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 data on gene-expression…
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…

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…

Integrity
Data

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…

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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…

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
Desktop

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…

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…

GPODE
Desktop

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…

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…

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,…

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…

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…

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…

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…

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…

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).…

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…

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…

NLNET
Desktop
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…

CABERNET
Desktop
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…

CYRENE
Desktop

CYRENE

Focuses on the study of cis-regulatory genomics and gene regulatory networks.…

Focuses on the study of cis-regulatory genomics and gene regulatory networks. The CYRENE Project has three components: a cisGRN-Lexicon, a cisGRN-Browser, and the Virtual Sea Urchin software system…

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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…

Pathway Flow
Web

Pathway Flow

Interprets omics lists in the context of metabolic pathway and regulatory…

Interprets omics lists in the context of metabolic pathway and regulatory networks using a statistical model for flow within the networks. Pathway Flow allows to visualized statistical results for…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

ENNET
Desktop

ENNET

An algorithm for Gene Regulatory Network inference from mRNA expression data.…

An algorithm for Gene Regulatory Network inference from mRNA expression data. ENNET method relies on the boosting of regression stumps combined with a relative variable importance measure for the…

DIRAC
Desktop

DIRAC Differential Rank Conservation

Provides quantitative measures of how network rankings differ either among…

Provides quantitative measures of how network rankings differ either among networks for a selected phenotype or among phenotypes for a selected network. DIRAC permits one to assess combinatorial…

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…

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…

SINCERITIES
Desktop
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…

GRENDEL
Desktop

GRENDEL Gene REgulatory Network Decoding Evaluations tooL

An open and extensible software toolkit. GRENDEL generates random gene…

An open and extensible software toolkit. GRENDEL generates random gene regulatory networks according to user defined constraints on the network topology and kinetics. It then simulates the state of…

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…

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…

SPINE
Desktop

SPINE Signaling-regulatory Pathway INferencE

A framework for signaling-regulatory pathway inference. SPINE aims at…

A framework for signaling-regulatory pathway inference. SPINE aims at explaining gene expression experiments in which a gene is knocked out and as a result multiple genes change their expression…

HumanNet
Data

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…

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…

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…

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…

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…

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…

ARACNe-AP
Desktop
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…

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).…

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…

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…

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…

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…

GRN2SBML
Desktop

GRN2SBML

Provides a framework for the automated encoding of gene regulatory network…

Provides a framework for the automated encoding of gene regulatory network (GRN)-models in SBML in compliance with the specifications of the standard. Providing a graphical user interface, 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…

CyNetworkBMA
Desktop

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…

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…

GNW
Desktop

GNW GeneNetWeaver

A comprehensive method for in silico benchmark generation and performance…

A comprehensive method for in silico benchmark generation and performance profiling of network inference methods available to the community. In addition to the generation of detailed dynamical models…

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…

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miRTarVis
Desktop

miRTarVis

An interactive visual analysis tool that predicts targets of miRNAs from…

An interactive visual analysis tool that predicts targets of miRNAs from miRNA-mRNA expression profile data and visualizes the resulting miRNA-target interaction network. miRTarVis has intuitive…

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…

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…

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…

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…

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…

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…

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…

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…

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AtmiRNET
Web

AtmiRNET

A resource geared towards plant scientists for reconstructing regulatory…

A resource geared towards plant scientists for reconstructing regulatory networks of Arabidopsis miRNAs. By means of highlighted miRNA studies in target recognition, functional enrichment of target…

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…

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…

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…

PANDA
Desktop

PANDA Passing Attributes between Networks for Data Assimilation

A message-passing model using multiple sources of information to predict…

A message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to…

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…

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SATMD
Web

SATMD Staphylococcus aureus Transcriptome Meta-Database

A meta-database that contains the post-analysis data from all transcriptome…

A meta-database that contains the post-analysis data from all transcriptome experiments done in Staphylococcus aureus. SATMD contains all the genes identified as regulated by either a locus or a…

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…

ROBNCA
Desktop

ROBNCA ROBust Network Component Analysis

An iterative algorithm that explicitly models the possible outliers in the…

An iterative algorithm that explicitly models the possible outliers in the microarray data. An attractive feature of the ROBNCA algorithm is the derivation of a closed form solution for estimating…

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…

SIRENE
Desktop

SIRENE Supervised Inference of Regulatory Networks

A method for the inference of gene regulatory networks from a compendium of…

A method for the inference of gene regulatory networks from a compendium of expression data. The method decomposes the problem of gene regulatory network inference into a large number of local binary…

CompareSVM
Desktop

CompareSVM

A tool based on support vector machine (SVM) to compare different kernel…

A tool based on support vector machine (SVM) to compare different kernel methods for inference of GRN. For network with nodes (<200) and average (over all sizes of networks), SVM Gaussian kernel…

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…

G T A T C G C T A
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…

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…

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…

GeneFAtt
Desktop

GeneFAtt

A tool that can compute all attractors in synchronous dynamic models and…

A tool that can compute all attractors in synchronous dynamic models and asynchronous dynamic models. GeneFAtt is helpful for biologist to deep understand the genetic 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…

Netmes
Desktop

Netmes

An R software package that allows assessing the Gene Regulatory Network…

An R software package that allows assessing the Gene Regulatory Network Inference (GRNI) algorithms in detail by using several local and global network-based error measures in combination with an…

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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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

NARROMI
Desktop

NARROMI

Improves the accuracy of gene regulatory network (GRN) inference by combining…

Improves the accuracy of gene regulatory network (GRN) inference by combining ordinary differential equation-based recursive optimization (RO) and information theory-based mutual information (MI).…

SITPR
Desktop
MI3
Desktop

MI3

A statistical learning strategy. MI3 addresses three common issues in previous…

A statistical learning strategy. MI3 addresses three common issues in previous methods simultaneously: (1) handling of continuous variables, (2) detection of more complex three-way relationships and…

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…

cGRNB
Web
Desktop

cGRNB combinatorial Gene Regulatory Networks Builder

A web server for building combinatorial gene regulatory networks through…

A web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. The cGRNB enables two major…

CLR
Desktop

CLR Context Likelihood of Relatedness

Infers regulatory interactions between transcription factors and their targets…

Infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles. CLR demonstrates an average precision gain of 36% relative to the…

MRNet
Desktop

MRNet

A software overlay network that provides efficient multicast and reduction…

A software overlay network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. MRNet uses a tree of processes between the tool's…

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