SAFE

Spatial Analysis for Functional Enrichment
Categories: annotation, enrichment analysis, functional module detection, visualization
The Spatial Analysis for Functional Enrichment (SAFE) App allows users to generate comprehensive functional maps of networks by mapping local over/under-representation of functional attributes. These functional maps illustrate which parts of the network are associated with a given attribute and where are these parts located relative to other attributes. For more information: Baryshnikova, A. (2016). Systematic Functional Annotation and Visualization of Biological Networks. Cell Systems. [http://doi.org/10.1016/j.cels.2016.04.014]
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1.0.0.beta7

Works with Cytoscape 3.3

Release Notes

- Updated UI text for clarity and brevity. - Added domain report when exporting results from Step 4. - Added interpretation guidelines to neighborhood report. - Added visual indicator for when network visualization is being recomputed in Steps 2/4.

1.0.0.beta6

Works with Cytoscape 3.3

Release Notes

- Changed color scheme to red-blue (high-low). - Changed "annotation" to "attribute". - Added ability to export enrichment scores in Step 2. - Added ability to filter attribute/domain tables in Steps 2/4 based on current node selection. - Added support for remembering the last directory browsed when picking an attribute file. - Fixed bug where user can attempt to compute enrichment when no attribute file is selected. - Fixed bug where table columns are laid out incorrectly in Cytoscape 3.4. - First attribute is now pre-selected when building the enrichment landscape. - Added color legend for Step 2 enrichment. - Fixed bug where annotation files without a header are handled incorrectly. - Fixed bug where enrichment visualization is recomputed unnecessarily.

1.0.0.beta4

Works with Cytoscape 3.3

CYTOSCAPE 3

Version 1.0.0.beta7

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Released 18 Feb 2017

Works with Cytoscape 3.3

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