OmniPath

OmniPath: literature curated human signaling pathways
The OmniPath app provides an easy way to import networks from OmniPath web service into Cytoscape. OmniPath is a comprehensive collection of literature curated signaling pathways which, consisting of more than 50 resources, intended to combine all high quality, manually curated efforts. The web service at [http://omnipathdb.org/ omnipathdb.org] serves 4 major data sets: * Signaling pathways (the original OmniPath as described in [https://doi.org/10.1038/nmeth.4077 Turei et al 2016]); * Extra kinase-substrate interactions; * TF Regulons: TF-target gene interactions (as described in [https://doi.org/10.1101/337915 Garcia-Alonso et al 2018]); * miRNA-mRNA interactions; With the OmniPath Cytoscape app you can import the data sets above, and fine-tune your custom network by selecting any combinations of the more than 50 resources and filtering the interactions by direction or sign. In addition the interactions from TF Regulons you will be able to filter by confidence level (A-D). We also provide the networks translated to mouse or rat by gene homology. Please consider the licenses of the original resources. You may find them here: [http://omnipathdb.org/info] Don’t hesitate to contact us if you have any question regarding the data or you are experiencing issues while using the app: omnipath@googlegroups.com

2.0

Works with Cytoscape 3.1

Release Notes

New features: - added 57 annotation categories from 32 original resources, with more than 14 000 features (pathways, cellular localizations, disease associations and more) - access the papers reporting the selected interactions by 2 clicks (Omnipath -> PubMed references) - added basic style for nodes based on the type

1.2

Works with Cytoscape 3.1

Release Notes

fixed "permission denied" issue related to Windows machines

1.1

Works with Cytoscape 3.1

Release Notes

fixed "permission denied" issue related to Linux machines

1.0

Works with Cytoscape 3.1


CYTOSCAPE 3

Version 2.0

Released 15 Dec 2019

Works with Cytoscape 3.1

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