CroP – Coordinated Panels Visualization

 

CroP is a visualization tool aimed at highlighting patterns of data in networks integrated with temporal data and analyzing their behaviors over time through dynamic visualization models in a coordinated multiple views layout.

 

 

The primary objective of the development of CroP has been the analysis of biological datasets such as gene expression time-series, and as such it provides an integrated Gene Ontology database that matches data point names with known genes to list their proprieties.

 

 

Data can be analyzed at different levels of detail through the network, table and time curve visualizations, and multiple datasets can be uploaded and visualized simultaneously through different panels. The visualization panels can be switched, resized and moved in order to adapt the workspace to the data being analyzed or to specific queries from the user.

 

CroP is freely available for download below as an executable jar, along with sample datasets. The supported data formats and available functionalities are detailed in the user manual.

 

Download Links

 

 

Sample Dataset Setup
  • Select “Load Network” and then “Network File (.csv)” to load the Human PPI network file;
  • Select “Load Time-Series” then “Time-Series File (.csv)” to load the HIV-1 time-series file;
  • Choose “Filter” to not add genes that are not present in the network;
  • Visualizations can be dragged with the left mouse button and zoomed with the scroll wheel;
  • Cluster by variance and switch the number of clusters with the slider.

 

Publication

  • A. Cruz, P. Machado, and J. P. Arrais, “CroP-Coordinated Panel visualization for biological networks analysis,” Bioinformatics, 2019.

Author

António Cruz

Joel P. Arrais

Penousal Machado