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Notes

This repository was archived and will not be updated. The R and Python notebook updates will take place in https://github.com/cytoscape/cytoscape-automation/.

This is a repository for National Resource for Network Biology (NRNB) Google Season of Docs project named

Replacing GUI control tutorials to Jupyter Notebook and R Markdown

The work we've done

We have written notebook documents that automates the Cytoscape tutorial workflows in http://tutorials.cytoscape.org/ with R and Python. You can check the our project progress and the links to the commits with the links below. Our basic commit rule is Commit every tutorial slide.

Getting Started

Protocols

Cytoscape Apps

Data Visualization

Importing Networks and Tables

Network Analysis

Exporting and Publishing

There is still work to be done...

  • We prioritize the creation of notebooks using RCy3. Python notebooks with py2cytoscape are still almost untouched.
  • Python notebooks doesn't require natural language writing ability (Because the text is the same as that of RCy3), but we may need to add the missing functions in py2cytoscape.

Issue list (What is missing in CyREST, py2cytoscape, and Cytoscape Apps (stringApp etc.)

  • CyREST does not yet support the merge network function
  • py2cytoscape does not yet have RCy3's selectNodes equivalent cytoscape/py2cytoscape#97
  • stringApp retrieve enrichment command does not yet support Apps -> STRING Enrichment -> Retrieve functional enrichment equivalent
  • clusterMaker2 doesn't have a document about Commands RBVI/clusterMaker2#11
  • CyNDEx-2 app has not implemented CyCommands.
  • PSICQUIC Web Service Client app has not implemented CyCommands.
  • CyCommand or CyREST do not have a function to get the currently applied Style.

Technical writer and mentors

Writer

Mentors

About my achievements during Season of Docs

https://github.com/nrnb/gsod2019_kozo_nishida/wiki/My-achievements-during-Season-of-Docs-(Q-and-A-style)