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Cytoscape VS yEd

Compare Cytoscape VS yEd and see what are their differences

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Cytoscape logo Cytoscape

Cytoscape Official Web Site

yEd logo yEd

yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.
  • Cytoscape Landing page
    Landing page //
    2021-07-29
  • yEd Landing page
    Landing page //
    2022-07-16

Cytoscape videos

+ Add

Cytoscape Tutorial- Beginners Guide in Jupyter

More videos:

  • Review - MetScape App for Cytoscape: Creating and Viewing Correlation Networks
  • Review - Download a Sequence Similarity Network from the EFI, import it into Cytoscape and apply a layout

yEd videos

+ Add

yEd Graph Editor in 90 seconds

More videos:

  • Tutorial - yED Graph Editor Tutorial - Make flowcharts, trees, graph Freeware.

Category Popularity

0-100% (relative to Cytoscape and yEd)

Cytoscape

yEd

Diagrams
20 20%
Diagrams
80% 80
Flowcharts
21 21%
Flowcharts
79% 79
Data Visualization
100 100%
Data Visualization
0% 0
Wireframing
0 0%
Wireframing
100% 100

User comments

Share your experience with using Cytoscape and yEd. For example, how are they different and which one is better?
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Reviews

These are some of the external sources and on-site user reviews we've used to compare Cytoscape and yEd

Cytoscape Reviews

We have no reviews of Cytoscape yet.
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yEd Reviews

Best 7 Free Online XMind Alternatives for Windows
Another excellent tool that you can use for common and complex visual illustration is yEd. This aims to help users in terms of creating diagrams like UML, flowcharts, network diagram, org chart, and other process illustrations. With this XMind free alternative, you will find every icon and symbol you need for the aforementioned diagrams. On the other hand, users are...
Source: gitmind.com
40 Open Source, Free and Top Unified Modeling Language (UML) Tools
yEd is a desktop application that can be used to quickly and effectively generate high-quality diagrams. Users can create diagrams manually, or import their external data for analysis. yEd’s automatic layout algorithms arranges even large data sets with just the press of a button. yEd is freely available and runs on all major platforms: Windows, Unix/Linux, and Mac OS X.With...
Source: www.predictiveanalyticstoday.com

Social recommendations and mentions

Based on our record, Cytoscape seems to be more popular. It has been mentiond 11 times since March 2021. We are tracking product recommendations and mentions on various public social media platforms and blogs. They can help you identify which product is more popular and what people think of it.

Cytoscape mentions (11)

  • A Canadian payroll dependency chart
    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
  • Budō Lineage Tree: a community-driven database and interactive explorer
    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
  • Any advice on a community detection algorithm?
    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
  • Lost interactive graph (as in nodes + edges) editing tool
    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
  • Gephi – The Open Graph Viz Platform
    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
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yEd mentions (0)

We have not tracked any mentions of yEd yet. Tracking of yEd recommendations started around Mar 2021.

What are some alternatives?

When comparing Cytoscape and yEd, you can also consider the following products

Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.

draw.io - Online diagramming application

Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.

LucidChart - LucidChart is the missing link in online productivity suites. LucidChart allows users to create, collaborate on, and publish attractive flowcharts and other diagrams from a web browser.

KeyLines - The JavaScript toolkit for graph visualization

PlantUML - PlantUML is an open-source tool that uses simple textual descriptions to draw UML diagrams.

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