• Fix to work with Cytoscape 3.10

Minor bugfixes

Updates:

• PSICQUIC resources updated

Minor bugfixes

Update release

Bugfix release.

Bugfix release:

• Gene origin info from Ensembl was added.
• Update to STRING 11.0

Bugfix release:

Bugfix release

Bugfix release

New release that works only with Java 1.8 and Cytoscape 3.5+.

New features:

• String data files were upgraded to version 10.5.

Bug fix release.

Info will be added...

Improvements:

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

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

• Bug fixes

• Fix to work with Cytoscape 3.4.0

Some minor changes and fixes to work with ClueGO 2.2.4.

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.

A fix for Project saving.

Fix for Wiki Pathways update.

General update. Some fixes.

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.

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

Some bug fixes.

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

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.

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.

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.

• Some bugfixes.

• 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.

• 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)

CluePedia was adjusted to ClueGO 2.0.7.

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!

Some bug fixes.

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.

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

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!

Release for ClueGO 2.0.2 and Cytoscape 3.0.0. CluePedia supports now again the Cerebral Layout function provided by Cerebral. Some bug fixes and improvements. External network files can be now directly imported into CluePedia.

First official release for ClueGO 2.0.1 and Cytoscape 3.0.0

First release for ClueGO 2.0.0 and Cytoscape 3.0.0

Release for ClueGO 2.0.0beta1 and Cytoscape 3.0.0beta1