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

• "Basic Data Visualization"
  • [x] with Python , link to the commits
  • [x] with R , link to the commits
• "Differentially Expressed Genes"
  • [ ] with Python
  • [x] with R , link to the commits

Protocols

Cytoscape Apps

• stringApp
  • [ ] with Python
  • [x] with R , link to the commits
• WikiPathways App
  • [ ] with Python
  • [x] with R , link to the commits

Data Visualization

• Visualizing Data
  • [ ] with Python
  • [x] with R , link to the commits
• Network Layout
  • [ ] with Python
  • [x] with R , link to the commits
• Custom Graphics and Labels
  • [ ] with Python
  • [x] with R (Already written by the mentor)

Importing Networks and Tables

• Loading Networks
  • [ ] with Python
  • [x] with R , link to the commits
• Importing Data From Tables
  • [x] with Python , link to the commits
  • [x] with R , (Already written by the mentor)
• Importing Network From Table
  • [ ] with Python
  • [x] with R , link to the commits
• Identifier Mapping
  • [ ] with Python
  • [x] with R , (Already written by the mentor)

Network Analysis

• Differentially Expressed Genes Network Analysis
  • [ ] with Python
  • [ ] with R
• Affinity Purification-Mass Spectrometry Network Analysis
  • [ ] with Python
  • [x] with R , (Already written by the mentor)
• Variant Data Analysis
  • [ ] with Python
  • [x] with R , (Already written by the mentor)
• EnrichmentMap Pipeline
  • [ ] with Python
  • [x] with R , (Already written by Ruth Isserlin)
• Functional Enrichment
  • [ ] with Python
  • [ ] with R link to the commits
• Filtering by Selection
  • [ ] with Python
  • [ ] with R

Exporting and Publishing

• Saving Results
  • [x] with Python , link to the commits
  • [x] with R , link to the commits

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 https://github.com/cytoscape/py2cytoscape/issues/97
• [ ] stringApp retrieve enrichment command does not yet support Apps -> STRING Enrichment -> Retrieve functional enrichment equivalent
• [ ] clusterMaker2 doesn't have a document about Commands https://github.com/RBVI/clusterMaker2/issues/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

• https://github.com/kozo2

  Mentors

• https://github.com/AlexanderPico
• https://github.com/khanspers

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)