Below you will find pages that utilize the taxonomy term “cytoscape”
Blog
Salmonella - Host Interaction Network - A Detailed, Better Visualization
We’re almost done with the analyses and we’re making the final visualization of the network. As I previously posted, the network was clustered and visualized by time points. After that, we have done several more analyses and here I report how we visualized them. I’m going to post more about how we did the analyses separately.
First, the nodes are grouped into experimental and not experimental (PCSF nodes). This can easily be done by parsing experimental network output and network outputs of PCSF.
Blog
Network Clustering with NeAT - RNSC Algorithm
As we have obtained proteins at different times points from the experimental data, then we have found intermediate nodes (from human interactome) using PCSF algorithm and finally with a special matrix from the network that PCSF created, we have validated the edges and also determined edge directions using an approach which a divide and conquer (ILP) approach for construction of large-scale signaling networks from PPI data. The resulting network is a directed network and will be used and visualized for further analyses.
Blog
Network Visualization Using Cytoscape
Cytoscape is a nice tool to visualize network for better understanding and delivery. I used it for in silico data network visualization and the result was really pretty. Now, I have networks constructed using experimental data from HPN-DREAM Challenge.
In this post, I want to demonstrate how to visualize a network with scores. I’m using Cytoscape 2.8 on Ubuntu 12.
First, the network will be read from a SIF file which is default format of Cytoscape for networks.
Blog
In silico Network Inference Last Improvements and Visualization of Result in Cytoscape
I’m almost done with the analysis of in silico data, although I need to decide if I need further analysis with the inhibiting parent nodes in the network. Last, I couldn’t filter out duplicate edges, which were scored differently. Now, with some improvements in the script, low scores duplicates are filtered and there is a better final list of edges which is ready to be visualized.
I also tried visualizing it on Cytoscape.