AutoAnnotate

Finds clusters and visually annotates them with labels and groups.
*This App is part of the [https://apps.cytoscape.org/apps/enrichmentmappipelinecollection EnrichmentMap Collection].* Finds clusters and visually annotates them with labels and groups. These visualizations provide a concise visual summary which is helpful for network analysis and interpretation. Features: * Automates running clusterMaker2 to generate clusters. (Or provide your own clusters by selecting any node attribute.) * Automatically generates cluster labels based on word frequencies of selected attributes. * Manages multiple “Annotation Sets” and easily switches between them. * Change the look of the annotations using several display options. * Cluster-aware layouts. * Automatically group and collapse clusters. Creates a simplified view by collapsing each cluster into a “meta-node” and collapsing edges between clusters into a single “meta-edge”. * Allows to manually create and update clusters. * Originally designed and used to annotate Enrichment Maps but applicable to any type of network including PPI, pathways, or Social networks. Warning > Versions of AutoAnnotate prior to version 1.3.3 are not fully compatibile with Cytoscape 3.8. > If you are having issues please upgrade to the latest version. Warning > Versions of AutoAnnotate prior to version 1.3.0 are incompatible with the latest version of > clusterMaker2. If you are having issues running AutoAnnotate please upgrade to the latest > version. Links: * [http://autoannotate.readthedocs.io User Guide] * [http://f1000research.com/articles/5-1717/v1 F1000 Research Software Tool Article] * [https://github.com/BaderLab/AutoAnnotateApp Code Repository] [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.883467.svg)](https://doi.org/10.5281/zenodo.883467)

1.5.1

Works with Cytoscape 3.9

Release Notes

* bug fixes

1.5.0

Works with Cytoscape 3.9

Release Notes

* UI updates to the AutoAnotate creation dialog. * Option to label clusters using the name of the most significant node in the cluster. * New slider that alows to choose the granularity of the clusters. * Support for using the MCODE app to find clusters in the network. * Thumbnail view at the bottom of the cluster panel. * Slider at bottom of cluster panel that allows to show/hide nodes according to their significance. * Better integration with EnrichmentMap. * Advanced options section in the Display Options panel. * Bug fixes.

1.4.1

Works with Cytoscape 3.9

Release Notes

* Fix for issue where annotations created in 1.3 would not load correctly in 1.4

1.4.0

Works with Cytoscape 3.9

Release Notes

* Support for color palettes. * New display option for cluster padding. * Summary networks have improved attribute aggregation. * Attribute aggregation now works for edges as well as nodes. * There is a new settings dialog that shows when creating a summary network. There is no longer a need to go into the group settings. * Aggregation settings can be specified for each individual column. * New aggregators for EnrichmentMap attributes. * Improved support for hidden nodes and edges. * Hiding nodes causes the clusters to resize to the visible nodes. * Hidden nodes and edges are ignored by clustering algorithms. * Bug Fixes

1.3.5

Works with Cytoscape 3.8

Release Notes

* Creating a summary network is much faster. * Bug fixes.

1.3.4

Works with Cytoscape 3.8

Release Notes

* Add "minimum word occurrence" option when creating labels. * Display panel: add "min font size" slider when "scale font by cluster size" is on. * Allow CoSE layout to run on selected nodes. * Update to Java 11. * Bug fixes.

1.3.3

Works with Cytoscape 3.8

Release Notes

Bugfix release to fix incompatibility with Cytoscape 3.8.

1.3.2

Works with Cytoscape 3.7

Release Notes

* Adds buttons and menu items to access the WordCloud excluded words and delimiters dialogs. * Add argument to layout command.

1.3

Works with Cytoscape 3.7

Release Notes

Requires Cytoscape 3.7 * Drawing annotations is much faster * Word wrap feature for cluster labels * New cluster-aware layouts * New feature: copy annotations to another network * Support for column namespaces * New “reset defaults” button in creation dialog * The “annotate” command now returns JSON * Cleaner “quick start” panel * Cleaner “display options” panel * Cleaner menu layouts * Several bug fixes

1.2

Works with Cytoscape 3.4

Release Notes

* Quick start for new users. * Streamlined display options panel. * Ability to change annotation colors. * Support for hidden nodes. * Option to create clusters for singleton nodes. * New commands for automating AutoAnnotate from CyREST. * Fixes for flickering annotations and performance issues.

1.1.0

Works with Cytoscape 3.3

Release Notes

* Added "Create Summary Network" feature because it is much faster than "Collapse All". * Added status bar to cluster panel. * Added "Display Creation Paramters..." feature. * Changed the look of the checkmarks in the "collapsed" column. * Bug fixes.

1.0.1

Works with Cytoscape 3.3

Release Notes

Bug-fix release that allows AutoAnnotate to work properly with Cytoscape 3.4.

1.0.0

Works with Cytoscape 3.3

Apps that depend on this release


CYTOSCAPE 3

Version 1.5.1

License Click here

Released 29 May 2024

Works with Cytoscape 3.9

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