Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data
Sign Up to like & getrecommendations! Published in 2021 at "Computational and Structural Biotechnology Journal"
DOI: 10.1016/j.csbj.2021.05.022
Abstract: Genome-scale mechanistic models of pathways are gaining importance for genomic data interpretation because they provide a natural link between genotype measurements (transcriptomics or genomics data) and the phenotype of the cell (its functional behavior). Moreover,… read more here.
Keywords: genome scale; cytoscape; bioconductor; mechanistic modeling ... See more keywords
A Cytoscape app for motif enumeration with ISMAGS
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DOI: 10.1093/bioinformatics/btw626
Abstract: Summary: We present a Cytoscape app for the ISMAGS algorithm, which can enumerate all instances of a motif in a graph, making optimal use of the motif's symmetries to make the search more efficient. The… read more here.
Keywords: cytoscape; cytoscape app; motif enumeration; ismags cytoscape ... See more keywords
Comparing protein structures with RINspector automation in Cytoscape.
Sign Up to like & getrecommendations! Published in 2018 at "F1000Research"
DOI: 10.12688/f1000research.14298.1
Abstract: Residue interaction networks (RINs) have been shown to be relevant representations of the tertiary or quaternary structures of proteins, in particular thanks to network centrality analyses. We recently developed the RINspector Cytoscape app, which couples… read more here.
Keywords: protein structures; automation cytoscape; cytoscape; comparing protein ... See more keywords
Visualize omics data on networks with Omics Visualizer, a Cytoscape App.
Sign Up to like & getrecommendations! Published in 2020 at "F1000Research"
DOI: 10.12688/f1000research.22280.2
Abstract: Cytoscape is an open-source software used to analyze and visualize biological networks. In addition to being able to import networks from a variety of sources, Cytoscape allows users to import tabular node data and visualize… read more here.
Keywords: visualize omics; omics visualizer; app; omics data ... See more keywords
CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks
Sign Up to like & getrecommendations! Published in 2017 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms18091880
Abstract: Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial… read more here.
Keywords: protein; ontology; cytoscape; analysis ... See more keywords
MSClustering: A Cytoscape Tool for Multi-Level Clustering of Biological Networks
Sign Up to like & getrecommendations! Published in 2022 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms232214240
Abstract: MSClustering is an efficient software package for visualizing and analyzing complex networks in Cytoscape. Based on the distance matrix of a network that it takes as input, MSClustering automatically displays the minimum span clustering (MSC)… read more here.
Keywords: msclustering cytoscape; cytoscape tool; cytoscape; multi level ... See more keywords