tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.

Module extraction software tools | Pathway analysis

A central goal of systems biology is to elucidate the structural and functional architecture of the cell. To this end, large and complex networks of molecular interactions are being rapidly generated for humans and model organisms. A recent focus of…
ResponseNet
Web

ResponseNet

A computational framework that identifies high-probability signaling and…

A computational framework that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins or genes,…

SANDY
Desktop
Web

SANDY

An approach for the statistical analysis of network dynamics combining…

An approach for the statistical analysis of network dynamics combining well-known global topological measures, local motifs and newly derived statistics. SANDY also examines the sub-networks locally…

cMonkey
Desktop

cMonkey

Identifies conditionally co-regulated modules of genes (biclusters). cMonkey…

Identifies conditionally co-regulated modules of genes (biclusters). cMonkey integrates various orthogonal pieces of information which support evidence of gene co-regulation, and optimizes biclusters…

DIAMOnD
Desktop

DIAMOnD DIseAse MODule identification algorithim

Aims to fill gap by analyzing the network properties of a comprehensive corpus…

Aims to fill gap by analyzing the network properties of a comprehensive corpus of 70 complex diseases. DIAMOnD allows to uncover the disease module associated with a particular phenotype. This…

MEMo
Desktop

MEMo Mutually Exclusive Modules in cancer

A method for identifying mutually exclusive driver networks in cancer. MEMo…

A method for identifying mutually exclusive driver networks in cancer. MEMo identifies networks defined by three properties: first, member genes are recurrently altered via somatic mutation or copy…

MITHrIL
Algorithm

MITHrIL Mirna enrIched paTHway Impact anaLysis

An algorithm developed for the analysis of signaling pathways. MITHrIL augments…

An algorithm developed for the analysis of signaling pathways. MITHrIL augments pathways with missing regulatory elements, such as microRNAs, and their interactions with genes. The method takes as…

jActiveModules
Desktop

jActiveModules

Finds clusters where member nodes show significant changes in expression…

Finds clusters where member nodes show significant changes in expression levels. jActiveModules is a plugin that searches a molecular interaction network to find expression activated subnetworks.…

Multi-species…
Desktop

Multi-species cMonkey

An algorithm for the simultaneous biclustering of heterogeneous…

An algorithm for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and…

PinnacleZ
Desktop

PinnacleZ

Identifies subnetworks which can discriminate given conditions according to PPI…

Identifies subnetworks which can discriminate given conditions according to PPI network and gene expression data. PinnacleZ is a tool for classifying gene expression profiles by integrating gene…

HotNet
Desktop
Web

HotNet

A general algorithm for identifying high weight subnetworks in a…

A general algorithm for identifying high weight subnetworks in a vertex-weighted network. HotNet was developed for identifying significantly mutated groups of interacting genes from large cancer…

PanGIA
Desktop

PanGIA Physical and Genetic Interaction Alignment

A plugin designed to integrate physical and genetic interactions into…

A plugin designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies "modules" as sets of proteins whose physical and genetic interaction data…

Paradigm
Desktop

Paradigm PAthway Representation and Analysis by Direct Reference on Graphical Models

A factor graph framework for pathway inference on high-throughput genomic data.…

A factor graph framework for pathway inference on high-throughput genomic data. A gene is modeled by a factor graph as a set of interconnected variables encoding the expression and known activity of…

BSCM
Desktop

BSCM Bicluster Sampled Coherence Metric

Allows users to determine which conditions and signals should be included in a…

Allows users to determine which conditions and signals should be included in a bicluster. BSCM provides a better way to simplify and interpret large amounts of expression data that come from multiple…

NetWalker
Desktop

NetWalker

A desktop application for functional analyses of large-scale genomics datasets…

A desktop application for functional analyses of large-scale genomics datasets within the context of molecular networks. The central analysis components, NetWalk and FunWalk, are novel random…

DiME
Desktop

DiME Disease Module Extraction

Identifies putative disease modules from biological networks. DiME is capable…

Identifies putative disease modules from biological networks. DiME is capable of extracting modules of coordinately expressed genes that point to key regulators in disease networks and thus provide a…

TieDIE
Desktop

TieDIE Tied Diffusion of Interacting Events

Computes a subnetwork of gene and protein interactions that connect genomic…

Computes a subnetwork of gene and protein interactions that connect genomic perturbations to gene expression changes characteristic of cancer subtypes. The pathways derived in this way predict…

RegMOD
Desktop

RegMOD

A method to detect disease related gene modules or dysfunctional pathways based…

A method to detect disease related gene modules or dysfunctional pathways based on global characteristics of interactome coupled with gene expression data. Moreover, this method can also be used for…

ClustEx
Desktop
Web

ClustEx

Discovers gene modules based on a set of genes in a known gene network. ClustEx…

Discovers gene modules based on a set of genes in a known gene network. ClustEx shows better performance than several available module identification tools by testing on the reference responsive gene…

MATISSE
Desktop

MATISSE Module Analysis via Topology of Interactions and Similarity SEts

A program for detection of functional modules using interaction networks and…

A program for detection of functional modules using interaction networks and expression data. MATISSE implements several algorithmic engines that analyze together expression and network data. Each of…

HC-PIN
Desktop

HC-PIN

A fast hierarchical clustering algorithm based on the local metric of edge…

A fast hierarchical clustering algorithm based on the local metric of edge clustering value which can be used both in the unweighted network and in the weighted network. The proposed algorithm HC-PIN…

Walktrap-GM
Desktop

Walktrap-GM

Identifies modules significantly enriched with cancer genes, their joint…

Identifies modules significantly enriched with cancer genes, their joint effects and promising candidate genes. The approach performs well when evaluated against similar tools and smaller overall…

diffuStats
Desktop

diffuStats

Contains a collection of diffusion kernels and scoring approaches that…

Contains a collection of diffusion kernels and scoring approaches that facilitates their computation and benchmarking. diffuStats is a package that consists of functions (i) to compute graph kernels,…

SAMBA
Desktop

SAMBA Statistical-Algorithmic Method for Bicluster Analysis

Enables a unified, high-level representation of heterogeneous biological…

Enables a unified, high-level representation of heterogeneous biological information and provide a means for the analysis of the biological system under study in light of very large functional…

ModuleDiscovere…
Desktop

ModuleDiscoverer

Identifies regulatory modules that can be identical (single-seed approach) or…

Identifies regulatory modules that can be identical (single-seed approach) or even more comprehensive (multi-seed approach). ModuleDiscoverer is an algorithm for the identification of regulatory…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.