Rene

Regulatory Network Enhancing Plugin - ReNE allows users to enhance standard KEGG/Reactome pathways wit
### NEWS: ReNE Paper Published ReNE paper has been published on Plos ONE Journal. The paper can be found at the following link: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0115585 (PlosONE ReNE Link)] ### ReNE ReNE (REgulatory Network Enhancing) Plugin allows users to enhance standard KEGG/Reactome pathways with information regarding: Transcription Factors, Proteins and MicroRNAs. Such enhancement allows to better understand/inspect possible regulatory motifs which involve entities commonly not presented into pathways. Enhanced pathways may be also exported for Boolean Network simulation, for further analysis with the BNToolkit (available for free on http://www.testgroup.polito.it/index.php/bio-menu-tools/item/208-boolean-regulatory-network-simulator). Plugin is still under development, so community suggestion and contributions are more than welcome. **Known Bug:** Installing ReNE after the installation of PetriScape results in a wild cytoscape loop. We are investigating this fact in collaboration with the Cytoscape Dev Team. While we are still searching for a definitive solution, if you experience any similar problem you can still correctly run ReNE by stopping the execution of PetriScape, then enabling ReNE.

1.94

Works with Cytoscape 3.0

Release Notes

methods to access MIRIAD have been updated

1.93

Works with Cytoscape 3.0

Release Notes

methods to access NCBI have been updated

1.92

Works with Cytoscape 3.0

Release Notes

Two new utility buttons: **Remove Proteins** -> allows for an easier handling of large networks by removing redundant proteins. The protein enhancement step is still required for miRNA targets computation. **Select Nodes** -> allows to highlight a list of nodes in a network. The list of nodes must be passed as a CSV text file

1.91

Works with Cytoscape 3.0

Release Notes

Update! After few days of problems everything sounds ok now!! Changes: updated the URL of two repositories

1.9

Works with Cytoscape 3.0

Release Notes

Bug Fixes and Enhancements

1.7.2

Works with Cytoscape 3.0


1.71

Works with Cytoscape 3.0

Release Notes

Bug fix and various improvements

1.6

Works with Cytoscape 3.0

Release Notes

Big update here! New feature: **External mirna enhancing** This new feature allows to introduce in the enhanced network external miRNAs that target genes/tfs. The filtering of miRNA target (already available for the intronic mirna target enhancement) is available for this option. New feature: **Utilities** Duplicate nodes: their merging automatically removes duplicated edges Undefined nodes: their removal is now a optional task. Users may remove undefined nodes only by pressing the proper button. Many bug fixes including: - mirna edges now properly target proteins instead of genes - set a slower timing for uniprot queries (previous one was too much fast, resulting in temporal ban from uniprot service) - custom network importing is now more reliable. Fixed possible misbehaviour of custom labels. - etc. improvement in speed, optimization

1.5

Works with Cytoscape 3.0

Release Notes

Bugfixes **New Feature** Importing custom pathways is now easier. Users can define -from any custom network- the label of the column containing gene symbols. So when a custom network is imported, original data are correctly retrieved for ReNE enhancing. **Updates in Boolean Rule generation** Now the output file is properly formatted for the new SatSolver implemented in BNToolkit.

1.3

Works with Cytoscape 3.0

Release Notes

Bugfixes Updated repositories' url

1.2

Works with Cytoscape 3.0

Release Notes

Bugfixes and Updates. Now the plugin correctly prints out documents properly formatted for BN Toolkit Updated the miRIAD text parser for reading miRIAD data in the new format.

1.1

Works with Cytoscape 3.0

Release Notes

Rene is now able to import Custom .owl and .xgmml file describing your own pathway to enhance.

1

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 1.94

License Click here

Released 16 Mar 2017

Works with Cytoscape 3.0

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