Table of contents
Open-source
Cytoscape is open-source software, making it freely accessible for users to download, use, and modify according to their needs. This encourages a community-driven approach to development and problem-solving.
Extensive Plugin Support
Cytoscape offers a vast library of plugins for extending its functionality. This adaptability allows users to tailor the tool to meet specific research or enterprise requirements, enhancing its versatility.
Comprehensive Visualization
It provides strong network visualization capabilities, allowing users to effectively analyze complex biological or general networks with intuitive graphical representations.
Integration Capabilities
Cytoscape can be integrated with other tools and data formats, enhancing its utility in various workflows and allowing seamless incorporation into existing data analysis pipelines.
Community and Documentation
The software has an active community and extensive documentation, making it easier for new users to get support and learn how to maximize its features.
We have collected here some useful links to help you find out if Cytoscape is good.
Check the traffic stats of Cytoscape on SimilarWeb. The key metrics to look for are: monthly visits, average visit duration, pages per visit, and traffic by country. Moreoever, check the traffic sources. For example "Direct" traffic is a good sign.
Check the "Domain Rating" of Cytoscape on Ahrefs. The domain rating is a measure of the strength of a website's backlink profile on a scale from 0 to 100. It shows the strength of Cytoscape's backlink profile compared to the other websites. In most cases a domain rating of 60+ is considered good and 70+ is considered very good.
Check the "Domain Authority" of Cytoscape on MOZ. A website's domain authority (DA) is a search engine ranking score that predicts how well a website will rank on search engine result pages (SERPs). It is based on a 100-point logarithmic scale, with higher scores corresponding to a greater likelihood of ranking. This is another useful metric to check if a website is good.
The latest comments about Cytoscape on Reddit. This can help you find out how popualr the product is and what people think about it.
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 / over 2 years 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: about 3 years 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 3 years 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 4 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 4 years ago
The formatting stuff was all in Cytoscape, which is a pretty sick program for graph stuff. Source: over 4 years ago
Protein interaction networks: Cytoscape. Source: over 4 years ago
Have you had a look at Cytoscape? I think this could work for what you're doing. It has a lot of layout options https://cytoscape.org. Source: over 4 years ago
Also if you don't need to embed it in a webpage you can just use cytoscape. Source: almost 5 years ago
What about this one? https://cytoscape.org/. Source: about 5 years ago
Hi! I'm looking for software that can map biological pathways and from several posts I found on ReasearchGate and Biostars, it seems like Cytoscape and PathVisio are the major players here. So I want to know what is the differences and which might be better for my need. PathVisio claimed that these are very different programs and it also mentioned that "PathVisio sees pathways as drawings, not as graphs. This... Source: about 5 years ago
Do you know an article comparing Cytoscape to other products?
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Is Cytoscape good? This is an informative page that will help you find out. Moreover, you can review and discuss Cytoscape here. The primary details have not been verified within the last quarter, and they might be outdated. If you think we are missing something, please use the means on this page to comment or suggest changes. All reviews and comments are highly encouranged and appreciated as they help everyone in the community to make an informed choice. Please always be kind and objective when evaluating a product and sharing your opinion.
