CluePedia

CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data
* Please note that **CluePedia** depends on the **[http://apps.cytoscape.org/apps/cluego ClueGO]** plugin! The CluePedia Cytoscape plugin is a search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data. Genes, proteins and miRNAs linked based on in silico and/or experimental information are integrated into a network with ClueGO terms/pathways. Interrelations within each pathway can be investigated and new potential associations may be revealed through gene/miRNA enrichments. A pathway-like visualization can be created using the Cerebral plugin layout. Combining all these features is essential for data interpretation and the generation of new hypotheses. The CluePedia Cytoscape plug-in is user friendly and has an expressive and intuitive visualization.

1.3.5

Works with Cytoscape 3.2

Release Notes

Bug fix release.

1.3.4

Works with Cytoscape 3.2

Release Notes

Info will be added...

1.3.3

Works with Cytoscape 3.2

Release Notes

Improvements: - Show ontology tree relations in addition to Kappa Score links - Rebuild ontology relations from selected terms up to the root (shortest way).

1.3.2

Works with Cytoscape 3.2

Release Notes

Bug fixes: - Nested network style was not updated - OpenCL double-float problem. In certain graphic card driver versions a stricter usage of data types is required. - Gene shape selection for multiple lists of markers was applied only to the first and the last cluster/list. - GEO direct search was not working due to ncbi link protocol change http->https Improvements: - Additionally to the kappa score edges, now also the ontology hierarchy edges from the .obo can be displayed between GO terms (new feature added as button in the CluePedia tool bar) - Improved network update behavior and speed - Edge types and colors for negative or positive associations can be customized now - New analysis suggestions and explanations included as help button - Groups loaded from GEO were improved to show additional features

1.2.6

Works with Cytoscape 3.2

Release Notes

* Bug fixes

1.2.5

Works with Cytoscape 3.2

Release Notes

* Fix to work with Cytoscape 3.4.0

1.2.4

Works with Cytoscape 3.2

Release Notes

Some minor changes and fixes to work with ClueGO 2.2.4.

1.2.3

Works with Cytoscape 3.2

Release Notes

STRING files can be directly updated now via CluePedia. The Biomart is still offline so the automatic update of Ensembl ids is at the moment not possible. Since STRING mainly uses Ensembl ids we will have to wait until Biomart has found a new home.

1.2.2

Works with Cytoscape 3.2

Release Notes

A fix for Project saving.

1.2.1

Works with Cytoscape 3.2

Release Notes

Fix for Wiki Pathways update.

1.2.0

Works with Cytoscape 3.2

Release Notes

General update. Some fixes.

1.1.7

Works with Cytoscape 3.0

Release Notes

Added GEO search/download support (for Human only at the moment). Updated STRING to v10.0. To keep the plugin small only Mouse and Human files are included. Data for other organisms can be requested or downloaded via ClueGO. Some bug fixes.

1.1.6

Works with Cytoscape 3.0

Release Notes

Update for Cytoscape 3.2.1, but it should still work with all the older versions. Some bug fixes.

1.1.5

Works with Cytoscape 3.0

Release Notes

Update for Cytoscape 3.2.0, but it should still work with all the older versions.

1.1.4

Works with Cytoscape 3.0

Release Notes

New features: * New GUI improvements of the CluePedia layout options that are now organized into tool bars. * A new layout button was added to hide genes that have no interaction to any other genes. * A help icon was added to the new tool bar to explain the layout features of CluePedia.

1.1.3

Works with Cytoscape 3.0

Release Notes

New features: * The percentage of visible genes (in the current network) per term/pathway can now be visualized as a pie chart on the term/pathway, as well as the percentage of genes from different clusters contributing to the term/pathway in case the "View Style Settings" are set to "Cluster". * There is now a new option to show all shared genes among the term/pathways, but it only works if the ClueGO network was created with a CluePedia "gene per term threshold" > 0 (best would be 100 to 500 but it slows down Cytoscape) in the new "CluePedia Options" section in ClueGO. By default the CluePedia "gene per term threshold" is set to 0 (swiched off) to have the maximum performance of Cytoscape.

1.1.2

Works with Cytoscape 3.0

Release Notes

New features: * Groups of genes/term can now be saved and are added as "Group" to the ontology selection table (ClueGO). * Groups of links can now be saved and are added as "CluePedia_EdgeGroup" to the Edge Link Files table (CluePedia). * CluePedia can be started now without inital genes from a Cluster (empty network) -> can be useful to created custom gene/term networks. * Two additional visualization check buttons were added. One to show shared genes between terms/pathways and one to show the selected links between all visible genes. * CluePedia can calculate now t-/MannWhitney tests for selected groups. For this an additional file with groups has to be loaded.

1.1.1

Works with Cytoscape 3.0

Release Notes

* Some bugfixes.

1.1.0

Works with Cytoscape 3.0

Release Notes

* CluePedia results can be **saved and restored** through ClueGO. * Input genes of ClueGO that were not found in any term or pathway can be now added to the network. * Some bugfixes.

1.0.9

Works with Cytoscape 3.0

Release Notes

* Various Bugfixes concerning gene node coloring (also in nested networks). * Improved vusialization: different shapes are available now for each gene input cluster * Improved speed for the term selection, gene-gene interrelation calculation and enrichments (multiple threads) * All genes from a term/pathway can be shown or hidden via the node menu (right mouse button the term/pathway node)

1.0.8

Works with Cytoscape 3.0

Release Notes

CluePedia was adjusted to ClueGO 2.0.7.

1.0.7

Works with Cytoscape 3.0

Release Notes

Bug fixed: The popup menu was not shown when (right mouse button) clicking on manually added nodes (also outside of ClueGO and CluePedia). To add links between manually added nodes CluePedia had to be deinstalled. This bug is fixed now!

1.0.6

Works with Cytoscape 3.0

Release Notes

Some bug fixes.

1.0.5

Works with Cytoscape 3.0

Release Notes

CluePedia (has to be used with ClueGO 2.0.5!) now supports PSICQUIC services. Additional services can manually added following the instructions in the psicquic-services.props file in the ./cluegoplugin/v2.0.5 folder. The PSICQUIC interactions can be downloaded for all genes/proteins or only for the selected ones from the network. Just select the genes of interest and click the refresh button. Then select the PSICQUIC service and click 'Get' to download the respective interactions.

1.0.4

Works with Cytoscape 3.0

Release Notes

CluePedia was verified to work with Cytoscape 3.0.1 and the correlation chart layout was improved.

1.0.3

Works with Cytoscape 3.0

Release Notes

Some bug fixes. A refresh button is added to avoid a cytoscape restart in case new files were externally added to CluePedia. Correlation charts can be displayed on edges when data is loaded. CluePedia should be always used with its corresponding ClueGO version!

1.0.2

Works with Cytoscape 3.0

Release Notes

Release for ClueGO 2.0.2 and Cytoscape 3.0.0. CluePedia supports now again the Cerebral Layout function provided by [http://www.pathogenomics.ca/cerebral/index.html Cerebral]. Some bug fixes and improvements. External network files can be now directly imported into CluePedia.

1.0.1

Works with Cytoscape 3.0

Release Notes

First official release for ClueGO 2.0.1 and Cytoscape 3.0.0

1.0.0

Works with Cytoscape 3.0

Release Notes

First release for ClueGO 2.0.0 and Cytoscape 3.0.0

1.0.0.beta1

Works with Cytoscape 3.0

Release Notes

Release for ClueGO 2.0.0beta1 and Cytoscape 3.0.0beta1

CYTOSCAPE 3

Version 1.3.5

License Click here

Released 17 Oct 2017

Works with Cytoscape 3.2

Download Stats Click here

CYTOSCAPE 2

Version 1.3

Released 3 May 2013

Works with Cytoscape 2.8

Download Stats Click here