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Unclassified tools | Pathway analysis

cMapper
Dataset

cMapper

Provides several types of information about different gene or biological…

Provides several types of information about different gene or biological contexts. cMapper is a gene-centric connectivity mapper for the European Bioinformatics Institute-Resource Description…

MAPPI-DAT
Desktop
BiNoM
Desktop

BiNoM Biological Network Manager

Provides functions for the import-export of some standard systems biology file…

Provides functions for the import-export of some standard systems biology file formats and a set of algorithms to analyze and reduce the complexity of biological networks. BiNoM provides the user…

NavMol
Desktop

NavMol

Allows users to interpret and edit small molecular structures. NavMol…

Allows users to interpret and edit small molecular structures. NavMol incorporates voice synthesizers to read information displayed on the computer screen, as well as chemoinformatics tools for the…

PPI3D
Web

PPI3D

Uses for searching, analyzing and modeling pairwise protein–protein…

Uses for searching, analyzing and modeling pairwise protein–protein interactions (PPI). PPI3D provides both summarized and detailed information on protein interactions in different forms including…

simPATHy
Desktop

simPATHy simulating PATHways

An R package that produces synthetic datasets useful to validate gene set…

An R package that produces synthetic datasets useful to validate gene set analysis methods focused on topological properties of biological networks. Given a graph structure representing a biological…

RadNet
Web

RadNet Radicle Network

Provides coexpression networks for the Radicle (RAD) samples. RadNet is a…

Provides coexpression networks for the Radicle (RAD) samples. RadNet is a method developed for data visualization and mining. It provides a powerful resource to gain further understanding of the…

SPICi
Web

SPICi Speed and Performance In Clustering

Constructs clusters greedily, starting from local seeds that have high weighted…

Constructs clusters greedily, starting from local seeds that have high weighted degree, and adding nodes that maintain the density of the clusters. SPICi is based on a simpler cluster expansion…

ChloroKB
Dataset

ChloroKB

Provides a comprehensive view of chloroplast metabolism connected to whole-cell…

Provides a comprehensive view of chloroplast metabolism connected to whole-cell metabolism. ChloroKB is a network-oriented reconstruction of the metabolism of A. thaliana which takes spatial…

SPATKIN
Desktop

SPATKIN

Simulates biomolecular interactions in one or two-dimensions. SPATKIN is a…

Simulates biomolecular interactions in one or two-dimensions. SPATKIN is a standalone software including a network-free lattice-based method which is able to simulate membrane-associated processes,…

PAC
Desktop

PAC Partition-Assisted Clustering and Multiple Alignments of Networks

Identifies automatically cell populations in mass cytometry data closely…

Identifies automatically cell populations in mass cytometry data closely matching that of expert manual-discovery. PAC-MAN allows the management of very large mass cytometry datasets, which are…

KinView
Desktop

KinView Kinome Viewer

Places eukaryotic protein kinase cancer variants in the context of natural…

Places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the…

BioNetGen
Desktop

BioNetGen

Generates et simulates rule-based models of biochemical systems. BioNetGen is…

Generates et simulates rule-based models of biochemical systems. BioNetGen is an open source software that can be used for modeling a wide range of processes such as cell signaling or gene…

NACE
Web

NACE

An open access web oriented program. NACE implements method of evaluating the…

An open access web oriented program. NACE implements method of evaluating the efficiency of biological processes based on the analysis of the distribution of protein subcellular localization and…

BahramiEtAl2017
Algorithm

BahramiEtAl2017

Adds explicit membrane-interacting proteins to the Helfrich membrane elastic…

Adds explicit membrane-interacting proteins to the Helfrich membrane elastic description. BahramiEtAl2017 provides a simulation method.

NOA
Desktop

NOA Network Ontology Analysis

Implements the NOA algorithm for network-based enrichment analysis, which…

Implements the NOA algorithm for network-based enrichment analysis, which extends Gene Ontology annotations to network links, or edges. NOA facilitates the annotation and analysis of one or more…

PhosphoPath
Desktop

PhosphoPath

A Cytoscape app designed for the visualization and analysis of quantitative…

A Cytoscape app designed for the visualization and analysis of quantitative proteome and phosphoproteome data sets. PhosphoPath brings knowledge into the biological network by importing publically…

Cytoscape App…
Dataset

Cytoscape App Store

Offers multiple ways for users to discover Cytoscape applications. This tool…

Offers multiple ways for users to discover Cytoscape applications. This tool provides a featured apps section that invites new users to simply click on a featured app, read about it and, with a…

ACDC
Desktop

ACDC Attribute Clustering Dependent Communities

Detects community structure in protein sequence similarity network (SSN). ACDC…

Detects community structure in protein sequence similarity network (SSN). ACDC is an unsupervised method that utilizes attribute vector clustering and excludes user-tunable parameters. The software…

Schizo-Pi
Web

Schizo-Pi

Predicts protein–protein interactions (PPIs) on hub proteins. Schizo-Pi is…

Predicts protein–protein interactions (PPIs) on hub proteins. Schizo-Pi is based on a random forest model to classify the pairwise features as interacting or non-interacting. This web app would be…

PathwaysWeb
Desktop

PathwaysWeb

A resourced-based, well-documented web system that provides publicly available…

A resourced-based, well-documented web system that provides publicly available information on genes, biological pathways, Gene Ontology terms, gene-gene interaction networks (importantly, with the…

GFD-Net
Desktop

GFD-Net

Aims to analyze gene networks according to the network topology. GFD-Net is a…

Aims to analyze gene networks according to the network topology. GFD-Net is a Cytoscape application that can analyze a gene network based on Gene Ontology (GO) and calculate a quantitative measure of…

VertexSort
Desktop

VertexSort

Facilitates 'Vertex Sort' (VS) algorithm application to other…

Facilitates 'Vertex Sort' (VS) algorithm application to other networks. VertexSort allows the application of the VS algorithm to a graph to elucidate its hierarchical structure.

Cyclone
Desktop

Cyclone

Aims at facilitating the use of BioCyc, a collection of Pathway/Genome…

Aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. It interfaces easily…

TACO
Web

TACO TAble COmparison

Facilitates effective visual comparison of potentially large tabular datasets…

Facilitates effective visual comparison of potentially large tabular datasets over time. TACO is a visual comparison tool that calculates the difference between pairs of tabular data. Based on that,…

ndexr
Desktop

ndexr Network Data Exchange

Enables a seamless transition from data acquisition to statistical analysis.…

Enables a seamless transition from data acquisition to statistical analysis. Ndexr provides an interface to NDEx installations from within R. NDEx is an open-source software framework to manipulate,…

HCSA
Desktop

HCSA hyper-cube shrink algorithm

Identifies an interior point that is near-uniquely defined by the enzyme…

Identifies an interior point that is near-uniquely defined by the enzyme profile. HCSA incorporates enzyme abundance into the stoichiometric model. It is a method to mimic steady-state ordinary…

regNet
Desktop

regNet

Predicts the impact of gene expression alterations on user-defined target…

Predicts the impact of gene expression alterations on user-defined target genes. regNet is an R package that (i) learns a regulatory network from a large collection of paired gene expression and copy…

RaBooNet
Desktop

RaBooNet Random Boolean Network

Provides an analogy for predicting biological systems. RaBooNet allows…

Provides an analogy for predicting biological systems. RaBooNet allows creation, simulation, and prediction of random Boolean networks. Boolean networks are graphs (nodes and directed arcs) with…

PathCORE
Web
Desktop

PathCORE

Maps each gene in each feature to the one pathway in which it has the greatest…

Maps each gene in each feature to the one pathway in which it has the greatest estimated impact. PathCORE overlays curated knowledge after feature construction to help researchers interpret…

ProteinsPlus
Web

ProteinsPlus

Allows users to access and preprocess structural data for all kinds of life…

Allows users to access and preprocess structural data for all kinds of life science research, and gives an immediate visual impression of the overall protein structure and contained ligand molecules.…

Ara-BOX-cis
Web

Ara-BOX-cis

Provides interactive visualisations of the G-box regulatory network, a useful…

Provides interactive visualisations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations. Ara-BOX-cis allows user to look through and download…

PINTnet
Web

PINTnet

Constructs condition-specific pathway interaction network. PINTnet uses…

Constructs condition-specific pathway interaction network. PINTnet uses protein-protein interaction (PPI), closeness centrality and shortest paths. It can be used to characterize biological…

BIOCEMID
Desktop

BIOCEMID BioC Experimental Molecular Interaction Detection

Identifies passages with experimental methods for physical interactions between…

Identifies passages with experimental methods for physical interactions between proteins as an information retrieval search task. BIOCEMID takes a BioC article as input, processes it, and returns the…

Rintact
Desktop

Rintact

Parses the PSI-25 files generated by the IntAct data repository which collects,…

Parses the PSI-25 files generated by the IntAct data repository which collects, curates and stores thousands of protein interactions. Rintact is an R package which provides two main functions: (i)…

ppiStats
Desktop

ppiStats

Uses for the analysis of protein interaction data. PpiStats is developed as an…

Uses for the analysis of protein interaction data. PpiStats is developed as an explicit probability model and resultant likelihood method to estimate node degree on portions of the interactome…

OCSANA
Desktop

OCSANA Optimal Combinations of Interventions from Network Analysis

Identifies and prioritizes optimal and minimal combinations of interventions to…

Identifies and prioritizes optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes. OCSANA seeks to additionally minimize the side effects that a…

GeneNet
Desktop

GeneNet

The toolbox, available as command-line or with a graphical user interface,…

The toolbox, available as command-line or with a graphical user interface, enables biologists to assess connectivity among a set of genes of interest ('seed-genes') within a biological…

Sig2GRN
Desktop

Sig2GRN

Allows users to link the models of signaling pathway with gene regulatory…

Allows users to link the models of signaling pathway with gene regulatory networks (GRNs). Sig2GRN represents a plugin for the Cytoscape software. It is able to simulate the dynamics of the signaling…

XMRF
Desktop

XMRF

Allows users to learn the network structure from data acquired from various…

Allows users to learn the network structure from data acquired from various high-throughput genomics technologies. XMRF is an R software package that encodes models and estimation techniques for…

ROMA
Desktop

ROMA Representation Of Module Activity

Approximates the expression data of a gene set by its first principal…

Approximates the expression data of a gene set by its first principal component. ROMA is based on the simplest uni-factor linear model of gene regulation. It addresses the issue of quantifying the…

CyKEGGParser
Desktop

CyKEGGParser

Allows manipulation with KEGG pathway maps. CyKEGGParser operates on pathways…

Allows manipulation with KEGG pathway maps. CyKEGGParser operates on pathways derived from the KEGG pathway database. Along with basic functionality of parsing and visualization of KEGG pathway maps…

Netpredictor
Web
Desktop

Netpredictor

Predicts missing links in any given bipartite network. Netpredictor provides…

Predicts missing links in any given bipartite network. Netpredictor provides utilities to compute missing links in a bipartite and well as unipartite networks using Random Walk with Restart and…

tergm
Desktop

tergm

Provides a set of methods for analyzing and simulating network evolution thanks…

Provides a set of methods for analyzing and simulating network evolution thanks to exponential-family random graph models (ERGM). tergm is a R package that extends the statnet toolkit.

ergm
Desktop

ergm

Allows users to fit, simulate from, plot and evaluate exponential family random…

Allows users to fit, simulate from, plot and evaluate exponential family random graph models (ERGMs). ergm is a R package which aims to describe the local selection forces that shape the global…

KEGG.db
Desktop

KEGG.db

Provides detailed information about the latest version of the KEGG pathway…

Provides detailed information about the latest version of the KEGG pathway databases. KEGG.db is an R package that permits access to a set of annotation maps for KEGG assembled using data from the…

netReg
Desktop

netReg

Matches linear regression models using network-penalization. netReg treats…

Matches linear regression models using network-penalization. netReg treats dependency of the same transcription factors/metabolites, and biological relationships such as co-regulation.

PPInfer
Desktop

PPInfer

Identifies such proteins often involved in the same or similar biological…

Identifies such proteins often involved in the same or similar biological functions. PPInfer is an R Bioconductor package. It provides functions to give the regularized Laplacian matrix for a graph.…

NetSAM
Desktop

NetSAM Network Seriation And Modularization

Performs network seriation and modularization analysis. NetSAM can generate a…

Performs network seriation and modularization analysis. NetSAM can generate a file that can be used as an input for the one-dimensional network visualization tool NetGestalt or other network…

Wordom
Desktop

Wordom

Performs a systematic search of the shortest communication pathways that…

Performs a systematic search of the shortest communication pathways that traverse a protein structure. Wordom is a mixed Protein Structure Network (PSN) and Elastic Network Model (ENM)-based…

BioCor
Desktop

BioCor

Calculates a functional similarity measure between gene identifiers based on…

Calculates a functional similarity measure between gene identifiers based on the pathways described on KEGG and REACTOME. BioCor is an R package. It offers functions to calculate the similarity…

cisPath
Desktop

cisPath

Uses web browsers to visualize and manage protein-protein interaction (PPI)…

Uses web browsers to visualize and manage protein-protein interaction (PPI) networks. cisPath is an R package that offers functions as a method used to combine the PPI information generated from…

Dropout
Desktop

Dropout

A technique for reducing overfitting in large neural nets. Dropout provides a…

A technique for reducing overfitting in large neural nets. Dropout provides a way of approximately combining exponentially many different neural network architectures efficiently. The term…

CYCDECO
Desktop

CYCDECO

Allows users to determine both cycle and u-path bases. CYCDECO is a standalone…

Allows users to determine both cycle and u-path bases. CYCDECO is a standalone software that uses undirected unweighted graphs for calculating features such as a minimum cycle bases and the set of…

Domino
Desktop

Domino

Visualizes subsets together with associated data and relationships between…

Visualizes subsets together with associated data and relationships between them. Domino is a technique that allows users to explore, extract, and manipulate subsets of multiple item types at various…

A A A
Mouse IDGenes
Dataset

Mouse IDGenes Gene interactions in the developing mouse brain

Gathers information for genetic interactions in the developing mouse brain.…

Gathers information for genetic interactions in the developing mouse brain. Mouse IDGenes consists in a manually curated reference database for genetic interactions in the developing mouse brain…

setsApp
Desktop

setsApp

A Cytoscape app for users to handle groups of nodes and/or edges. setsApp…

A Cytoscape app for users to handle groups of nodes and/or edges. setsApp allows users to explore various combinations of nodes and edges and to save such selections for later uses. It supports…

MULE
Desktop

MULE Mining Uniquely Labeled Edgesets

Detects conserved interaction patterns in biological networks. MULE uses a…

Detects conserved interaction patterns in biological networks. MULE uses a graph simplification technique based on ortholog contraction, which is ideally suited to biological networks, to render this…

LineUp
Web
Desktop

LineUp

Provides visualization technique that uses bar charts. LineUp is a Java…

Provides visualization technique that uses bar charts. LineUp is a Java application for creating, analyzing, and comparing multi-attribute rankings. It offers interactive refinement of weights and…

BioUML
Desktop

BioUML

Allows building of virtual cell and virtual physiological human. BioUML is a…

Allows building of virtual cell and virtual physiological human. BioUML is a platform, providing access to databases and tools, that aims user to analyze omics technologies generated data. The…

Igraph
Desktop

Igraph

Creates and manipulates graphs. Igraph is a collection of network analysis…

Creates and manipulates graphs. Igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. It is intended to be as powerful and fast as possible to…

Disease complex
Desktop

Disease complex

Discovers disease related protein complexes. Disease complex integrates network…

Discovers disease related protein complexes. Disease complex integrates network propagation with an integer program algorithm designed to discover dense clusters with highly specific interactions.…

StemCellNet
Web

StemCellNet

A versatile web server for interactive network analysis and visualization.…

A versatile web server for interactive network analysis and visualization. StemCellNet rapidly generates focused networks based on a large collection of physical and regulatory interactions…

PROTON
Desktop

PROTON

Allows automatic and user-controlled reconstruction of biochemical systems from…

Allows automatic and user-controlled reconstruction of biochemical systems from molecular databases.

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