Search Results for "cytoscape"
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Showing 55 open source projects for "cytoscape"
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Cytoscape.js
Graph theory library for visualization and analysis
A fully featured graph library written in pure JS. Permissive open source license (MIT) for the core Cytoscape.js library and all first-party extensions. Used in commercial projects and open-source projects in production. Designed for users first, for both frontfacing app usecases and developer usecases. Highly optimized. Compatible with All modern browsers. Legacy browsers with ES5 and canvas support. ES5 and canvas support are required, and feature detection is used for optional... -
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genppi
GENPPI: standalone software for creating protein interaction networks
Our software GENPPI is efficient because, for example, it creates interaction networks from the central genome of 50 species/lineages of Corynebacterium, with an average size of 2200 genes, in less than 40 minutes, on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships between species and obtained in Average Nucleotide Identity (ANI) analyzes. Also, It allows the user to define how he intends to explore the... -
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ipycytoscape
A Cytoscape Jupyter widget
A widget enabling interactive graph visualization with cytoscape.js in JupyterLab and the Jupyter Notebook. -
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This project is a Moodle resource o Moodle activity with finality to build a relational diagram for social estudy of the social relationships between students from different schools this LMS.
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UFO-Cytoscape
Ontology-based semantic similarity calculation and visualization
... implemented a small number of the semantic similarity measures for only one type of biomedical ontology. Note that, the measures can be applied to all types of biomedical ontologies. In addition, each measure is dominant in different biomedical applications. In this study, we developed a Cytoscape app, named UFO, which unifies most of the proposed semantic similarity calculation and visualization for all types of biomedical ontology. -
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RWRMTN
Predicting disease-associated miRNAs on a miRNA-target gene network
..., we develop a Cytoscape app, named RWRMTN, to predict disease-associated microRNAs. RWRMTN can work on any microRNA-target gene network. Highly ranked microRNAs can be supported with evidence from literature. Then, they can be also visualized based on the rankings in relationships with the query disease and their target genes. In addition, automation functions are also integrated, which permits RWRMTN can be used from external tools -
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EntOpt Layout
Relative entropy optimization network layout plugin
The goal of this project is to implement a graph layout / network visualization algorithm as a Java plugin for Cytoscape (http://cytoscape.org/), using a recently published relative entropy optimization based method, called Unified Data Representation (Kovács IA et al. Sci Rep. 2015). If you are using the plugin, please cite: Ágg B, Császár A, Szalay-Bekő M, Veres DV, Mizsei R, Ferdinandy P, Csermely P and Kovács IA (2019) The EntOptLayout Cytoscape plug-in for the efficient visualization... -
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HGPEC
A tool for gene and phenotype prioritization and evidence collection
Finding gene-disease and disease-disease associations are important issues in the biomedical area and many prioritization methods have been proposed for this goal. Among these, approaches based on heterogeneous network of genes and phenotypes were considered state-of-the-art ones, which can use for diseases with/without known molecular basis. Here, we develop a Cytoscape plugin, namely HGPEC, based on a ran-dom walk with restart algorithm on a heterogeneous network of genes and phenotypes... -
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CyNetSVM is a tool developed in JAVA and integrated as a Cytoscape APP to predict clinical outcome and identify network bio-markers by integrating gene expression data and PPI data. The app can be installed directly from Cytoscape app store. We also provided the package at http://sourceforge.net/projects/netsvmjava/files/netSVM.zip/download The example data to test the package is available at http://sourceforge.net/projects/netsvmjava/files/Example.zip/download The user manual...
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Placnet
Placnet project
Plasmid Constellation Network project. Placnet is a new tools for plasmid analysis in NGS projects. Placnet has been written in Perl. It's been optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools. Please cite... -
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This package implements the algorithm bagging markov random field method with c++ together with Java interface. http://nar.oxfordjournals.org/content/41/2/e42.long Cytoscape App: BMRF-Net-CytoscapeV1.0.tar.gz https://sourceforge.net/projects/bmrfcjava/files/BMRF-Net%20Package/BMRF-Net-CytoscapeV1.0.tar.gz/download Source code and standalone version: BMRF-Net-standalone.tar.gz https://sourceforge.net/projects/bmrfcjava/files/BMRF-Net%20Package/BMRF-Net-standaloneV1.1.tar.gz/download...
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The complexity of cellular networks is an outstanding challenge for documentation, visualisation and mathematical modelling. In this project, we develop a new way to describe these networks that minimises the combinatorial complexity and allows an automatic visualisation and export of mathematical (ODE/rulebased) models.
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CytoscapeAlignmentDrawerPlugin
a Cytoscape plugin for visualizing SANA alignment
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CoNet
Find relationships between repeatedly observed items
CoNet is a Cytoscape plugin that detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data. It has been designed with (microbial) ecological data in mind, but can be applied in general to infer relationships between objects observed in different samples (for example between genes present or absent across organisms). -
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This project implements a Cytoscape plugin for viewing and manipulating pathway maps for metabolic models created by the Model SEED (http://www.theseed.org/models). See the "Files" area for README. See Project Homepage for Tutorial.
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PEANuTv3
This is a port of PEANuT to Cytoscape 3.x
This App is a port of the PEANuT plug-in to Cytoscape 3.2 and up. Authors: Falko Hofmann (2.x version) Viktor Senderov (porting to 3.x) PEANuT utilizes data from the following databases: - ConsensusPathDB - PathwayCommons - WikiPathways A publication is currently in preparation. PEANUT is designed to work in concert with the VIPER and COMFI. -
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cy2sbml
cy2sbml: Cytoscape 2 Plugin for SBML
cy2sbml is a plugin for the import and work with SBML files in Cytoscape 2. Latest releases https://github.com/matthiaskoenig/cy2sbml For Cytoscape 3 use cy3sbml https://github.com/matthiaskoenig/cy3sbml -
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PANET, a Cytoscape plugin is developed to efficiently analyze the robustness-related dynamics and feed-forward/feedback loop structures of biological networks. This is an advanced plugin of NetDS (http://netds.sourceforge.net/). We employed OpenCL library to make the time-consuming parts of NetDS are processed in parallel. Finally, in comparison to the original NetDS, PANET performed large-scale robustness calculation and feed-forward/feedback loop examination faster by several hundred times...
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PEANuT
A Cytoscape plugin for pathway enrichment analysis
PEANuT is a Cytoscape 2.8.3 plugin for pathway enrichment analysis. PEANuT utilizes data from the following databases: - ConsensusPathDB - PathwayCommons - WikiPathways The version for Cytoscape 3.x is available via http://sourceforge.net/projects/peanutv3/ A publication is currently in preparation. PEANUT is designed to work in concert with the VIPER and COMFI plugins. -
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RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.
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Viper
Cytoscape-plugin to find connections in networks
Viper is a plugin, that assists in finding all paths, up to a maximal length, between 2 or more nodes. -
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ExprEssence uses differential data (e.g. gene expression data) to highlight those links of a network, across which the largest changes can be observed comparing two experiments. * Please cite http://www.biomedcentral.com/1752-0509/4/164 * Tutorial: http://www.ibima.med.uni-rostock.de/warsow/ExprEssence.shtml
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cy2fluxviz
cy2fluxviz : Cytoscape 2 plugin for flux distribution visualization
cy2fluxviz - Cytoscape 2 Plugin for the visualization of flux distributions in networks. Latest releases from https://github.com/matthiaskoenig/cy2fluxviz -
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cy2sabiork
cy2sabiork: Cytoscape 2 Plugin for SabioRK
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This plugin allow to visualize several e.g. gene expression values simultanously using pie charts. * Please cite http://www.biomedcentral.com/1752-0509/4/164 *