QualCoder is free, open source software for qualitative data analysis. You can code text, images, audio and video, write journal notes and memos. Categorise codes in a tree-like hierarchical categorisation scheme. Coding for audio and video requires the VLC media player. VLC must be installed for QualCoder to work. Coder comparison reports can be generated for text coding. A graph displaying codes and categories can be generated to visualise the coding hierarchy. Most reports can be exported at html, open document text (ODT) or as plain text files.
QualCoder is one of the best CAQDAS I have used not just because it is free and open source but also because of the functionalities and constant improvements.
I really like using QualCoder 3.0 for its ease of use and intuitive interface.
The software is efficient and powerful to perform the content analysis task. It allows you to follow the categories and classifications clearly. Facilitates thematic analysis. It is an excellent technology to implement a qualitative methodology. It is a 100% recommended software.
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.
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 / 5 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: about 1 year 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
MAXQDA - a professional software for qualitative and mixed methods data analysis
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Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.