SAFE

Spatial Analysis for Functional Enrichment

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

1.0.0.beta7 8 years ago

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 8 years ago

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 8 years ago

Works with Cytoscape 3.3


CYTOSCAPE 3

Version 1.0.0.beta7

License Click here

Released 18 Feb 2017

Works with Cytoscape 3.3

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