InsituNet

Analysis of in situ gene expression data in terms of spatial co-expression.
InsituNet converts *in situ* sequencing data into interactive network-based visualizations, where each transcript is a node in the network and edges represent the spatial co-expression relationships between transcripts. InsituNet profiles and facilitates comparison of different 2D tissue regions by identifying spatial co-expressions that occur between transcripts both significantly more, and less, than statistically expected, given the frequency of the transcripts in the tissue. *** **Published in:** [https://www.cell.com/cell-systems/pdf/S2405-4712(18)30107-8.pdf Cell Systems] **Please cite:** *Salamon, J, Lynn, D, Qian, X & Nilsson, M 2018, 'Network visualization and analysis of spatially aware gene expression data with InsituNet' Cell Systems, vol 6, pp. 1-5.* *** **Features** - Import spatially-resolved 2D gene expression datasets from csv files directly into Cytoscape - Interactively explore datasets within an OpenGL window embedded within the control panel - Select (irregularly-shaped) regions of interest for comparison to other regions - Statistical and thresholding options for assessment of co-expression significance - Network style based on proportion of transcripts and strength of relationship within selected areas - Continuous layout synchronization of generated networks to aid comparison. *** **Links** - [https://bitbucket.org/insitunet/insitunet/ Source code] - [https://bytebucket.org/insitunet/insitunet/wiki/InsituNet_Documentation.pdf Documentation (pdf)] - [https://sala6.bitbucket.io/ Documentation (html)] - [https://bitbucket.org/insitunet/insitunet/src/master/datasets/ Example datasets] - [https://sala6.bitbucket.io/#x1-240006 Tutorials] - [https://www.cell.com/cell-systems/pdf/S2405-4712(18)30107-8.pdf Publication]

1.0.4

Works with Cytoscape 3.2

Release Notes

Added various new features: - Legend may be scrolled using mouse - Network component selection automatically filters tissue view - Micrometer distance conversion more sensible - Control-click simulates right-click on tissue view - Saner sliding window defaults

1.0.3

Works with Cytoscape 3.2

Release Notes

- Removed deprecated features from shaders. - Improved compatibility with some MacOS OpenGL implementations. - Fixed pixel-um distance conversion.

1.0.2

Works with Cytoscape 3.2

Release Notes

Initial Release

CYTOSCAPE 3

Version 1.0.4

Released 24 Jan 2018

Works with Cytoscape 3.2

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