NetworkX VS Cytoscape

In the project we used Python lib networkx and a DiGraph object (Direct Graph). To detect a table reference in a Query, we use sqlglot, a SQL parser (among other things) that works well with Bigquery. - Source: dev.to / 3 months ago

If you program in Python, can use NetworkX for that. But it's probably a good idea to implement the basic algorithms yourself at least one time. Source: 5 months ago

For those wanting to play with graphs and ML I was browsing the arangodb docs recently and I saw that it includes integrations to various graph libraries and machine learning frameworks [1]. I also saw a few jupyter notebooks dealing with machine learning from graphs [2]. Integrations include: * NetworkX -- https://networkx.org/ * DeepGraphLibrary -- https://www.dgl.ai/ * cuGraph (Rapids.ai Graph) --... - Source: Hacker News / 7 months ago

Org-roam-ui is a great interactive visualization tool, but its main use is visualization. The hope of this library is that it could be part of a larger graph analysis pipeline. The demo provides an example graph visualization, but what you choose to do with the resulting graph certainly isn't limited to that. See for example networkx. Source: 12 months ago

Back in college, I had an assignment deadline coming up and I wanted to work on it in the train since I had an 8-hour journey ahead of me. It was about some analysis of graph data, which used a Python package called NetworkX. The train's WiFi didn't allow me to access their documentation because it apparently thought it was porn. Source: 12 months ago

Doing a bit more digging, it's using cytoscape[0] which is similar to graphviz. If you search your favorite search engine with "Cytoscape Session Viewer", you'll find many websites displaying the same type of graphs (select layout: circle). FYI, circo doesn't always output a circle. I recently created https://github.com/MegaManSec/SSH-Snake/blob/main/tools/SSH-Snake-dot-circo.png. - Source: Hacker News / 4 months ago

The YAML files are then parsed, and a CYJS file produced, which is a graph model. This is used directly in the web app, but can also be opened in the Cytoscape desktop app , and imported into Neo4j if desired. I can add additional "export" steps to the automated build process, so e.g. GraphML (yEd, Gephi) or DOT files (GraphViz, mermaid, etc) can be used for whatever purpose needed. Source: 11 months ago

Both Cytoscape and Gephi are options that you can try on Windows; both can run some classic community detection algorithms and can be extended with plugins. Personally, I'd recommend you to use igraph, which can be run as an R or python libraries. Then, about the specific algorithm, I have no experience on amino acid communities, but I would approach the issue thinking the properties that you would like to... Source: over 1 year ago

Two common GUI tools for analysis and editing of graph data are Gephi and Cytoscape. An older alternative starting with a P is Pajek, but I've never used it. Source: almost 2 years ago

I've been thinking that Gephi is getting long in the tooth. Has anybody tried Cytoscape? (https://cytoscape.org/) (DNS is SERVFAILing at the moment.) I use it for a combination of "no K" clustering (general exploration) and what's referred to in threat intelligence by the term of art "pivoting". - Source: Hacker News / about 2 years ago