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Gene network inference software tools | Pathway analysis

BNFinder
Desktop

BNFinder Bayesian Network Finder

Provides a more comprehensive method for inferring networks with predefined…

Provides a more comprehensive method for inferring networks with predefined error rate. BNFinder is a flexible tool for network topology learning from experimental data. It also introduces the…

BANFF
Desktop

BANFF BAyesian Network Feature Finder

An R package for gene network feature selection. BANFF provides a package of…

An R package for gene network feature selection. BANFF provides a package of posterior inference, model comparison, and graphical illustration of model fitting. The model was extended to a more…

EGAD
Desktop

EGAD Extending Guilt-by-Association by Degree

Predicts members of gene groups, assesses how well a gene network groups known…

Predicts members of gene groups, assesses how well a gene network groups known sets of genes, and determines the degree to which generic predictions drive performance. Two of the core features of…

Basset
Desktop

Basset

Applies convolutional neural networks (CNNs) to learn the functional activity…

Applies convolutional neural networks (CNNs) to learn the functional activity of DNA sequences from genomics data. Basset is a package to apply deep CNNs to learn DNA sequence activity. Basset…

Graphite Web
Web

Graphite Web

Combines topological and multivariate pathway analyses with an efficient and…

Combines topological and multivariate pathway analyses with an efficient and interactive system of network visualizations that allows an easy results interpretation. Graphite web is a public server…

FGNet
Desktop

FGNet Functional Gene Networks

An R/Bioconductor package that generates gene networks derived from the results…

An R/Bioconductor package that generates gene networks derived from the results of functional enrichment analysis (FEA) and annotation clustering. The sets of genes enriched with specific biological…

pathTiMEx
Desktop

pathTiMEx

A generative probabilistic graphical model that describes tumor progression as…

A generative probabilistic graphical model that describes tumor progression as a partially ordered set of mutually exclusive driver pathways. PathTiMEx employs a stochastic optimization procedure to…

FunRich
Desktop

FunRich FUNctionnal enRICHment analysis tool

Uses mainly for functional enrichment and interaction network analysis of genes…

Uses mainly for functional enrichment and interaction network analysis of genes and proteins. FunRich allows analysis to be depicted graphically in the form of Venn, Bar, Column, Pie and Doughnut…

GeneNet
Web

GeneNet

Designed for formalized description and automated visualization of gene…

Designed for formalized description and automated visualization of gene networks. The GeneNet system includes: database on gene network components, Java program for the data visualization.

D-Map
Web

D-Map

A web application capable of generating and manipulating advanced differential…

A web application capable of generating and manipulating advanced differential networks by combining state-of-the-art inference reconstruction methods with random walk simulations. With D-Map,…

GENIUS
Web

GENIUS Gene Networks Inference Using Signatures

A machine learning method to infer local and discriminative gene networks.…

A machine learning method to infer local and discriminative gene networks. GENIUS incorporates Gene Ontology annotations and thousands of microarrays experiments from Gene Expression Omnibus (GEO)…

caspo
Desktop

caspo Cell ASP Optimizer

Provides a logic-based implementation of the hypotesis-driven research loop in…

Provides a logic-based implementation of the hypotesis-driven research loop in systems biology. The caspo toolbox combines various steps: (i) learn a family of logical networks derived from a given…

RelExplain
Web

RelExplain

Analyzes a particular biological process bp in the context of a given network…

Analyzes a particular biological process bp in the context of a given network to unravel the relevant relationships of the involved genes in the process. RelExplain is a method designed to find…

PathwayNet
Web

PathwayNet

An integrated, scalable strategy for inferring multiple human gene interaction…

An integrated, scalable strategy for inferring multiple human gene interaction types that takes advantage of data from diverse tissue and cell-lineage origins. PathwayNet specifically predicts both…

FuseNet
Desktop

FuseNet

A Markov network formulation that infers networks from a collection of…

A Markov network formulation that infers networks from a collection of nonidentically distributed datasets. This approach is computationally efficient and general: given any number of distributions…

GNAT
Desktop
Web

GNAT Genetic Network Analysis Tool

Allows exploration of gene function and regulation in a tissue-specific manner.…

Allows exploration of gene function and regulation in a tissue-specific manner. GNAT simultaneously constructs co-expression networks for 35 distinct human tissues. Using a hierarchy which encodes…

Predictive…
Desktop

Predictive Networks

Enables the integration, navigation, visualization and analysis of gene…

Enables the integration, navigation, visualization and analysis of gene interaction networks. Predictive Networks allows biomedical researchers to evaluate experimentally derived gene lists in the…

GENIES
Web

GENIES Gene Network Inference Engine based on Supervised Analysis

Predicts unknown part of gene network from various types of genome-wide data in…

Predicts unknown part of gene network from various types of genome-wide data in the framework of supervised network inference. The originality of GENIES lies in the construction of a predictive model…

GRAPHITE
Desktop

GRAPHITE GRAPH Interaction from pathway Topological Environment

Gathers and makes easily available the contents of the four major pathway…

Gathers and makes easily available the contents of the four major pathway databases. GRAPHITE discriminates between different types of biological gene groups; propagates gene connections through…

lpNet
Desktop

lpNet

Aims at inferring biological networks, in particular signaling and gene…

Aims at inferring biological networks, in particular signaling and gene networks. For that lpNet takes perturbation data, either steady-state or time-series, as input and generates an LP model which…

BUS
Desktop

BUS

Calculates associations among genes (gene-networks) or between genes and some…

Calculates associations among genes (gene-networks) or between genes and some external traits (i.e. clinical). BUS is a package that can handle data with missing values using bootstrapping methods to…

NTW
Desktop

NTW

Predicts the gene-gene interaction network and identifies the direct…

Predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method. NTW includes the functions…

FuNeL
Desktop

FuNeL Functional Network Learning protocol

A protocol to infer functional networks from machine learning models. It is a…

A protocol to infer functional networks from machine learning models. It is a general approach that uses BioHEL, a rule-based evolutionary classifier, to describe the expression samples as a set of…

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Kiwi
Desktop
Web

Kiwi

Processes output data from gene-set analysis and integrates them with a network…

Processes output data from gene-set analysis and integrates them with a network structure such that the inherent connectivity between gene-sets, i.e. not simply the gene overlap, becomes apparent.…

Partek Pathway
Desktop

Partek Pathway

Offers a solution with more accurate results through the use of the Pathway…

Offers a solution with more accurate results through the use of the Pathway ANOVA statistical model. Partek Pathway integrates with Partek Genomics Suite allows to interactively browse the KEGG…

SEBINI
Desktop

SEBINI Software Environment for BIological Network Inference

Allows to deploy and evaluates algorithms used to reconstruct the structure of…

Allows to deploy and evaluates algorithms used to reconstruct the structure of biological regulatory and interaction networks. SEBINI provides a web-based environment that allows inference algorithms…

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