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
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.
- "Basic Data Visualization"
- with Python , link to the commits
- with R , link to the commits
- "Differentially Expressed Genes"
- with Python
- with R , link to the commits
- stringApp
- with Python
- with R , link to the commits
- WikiPathways App
- with Python
- with R , link to the commits
- Visualizing Data
- with Python
- with R , link to the commits
- Network Layout
- with Python
- with R , link to the commits
- Custom Graphics and Labels
- with Python
- with R (Already written by the mentor)
- Loading Networks
- with Python
- with R , link to the commits
- Importing Data From Tables
- with Python , link to the commits
- with R , (Already written by the mentor)
- Importing Network From Table
- with Python
- with R , link to the commits
- Identifier Mapping
- with Python
- with R , (Already written by the mentor)
- Differentially Expressed Genes Network Analysis
- with Python
- with R
- Affinity Purification-Mass Spectrometry Network Analysis
- with Python
- with R , (Already written by the mentor)
- Variant Data Analysis
- with Python
- with R , (Already written by the mentor)
- EnrichmentMap Pipeline
- with Python
- with R , (Already written by Ruth Isserlin)
- Functional Enrichment
- with Python
- with R link to the commits
- Filtering by Selection
- with Python
- with R
- Saving Results
- with Python , link to the commits
- with R , link to the commits
- 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.
- CyREST does not yet support the merge network function
- py2cytoscape does not yet have RCy3's
selectNodesequivalent cytoscape/py2cytoscape#97 - stringApp
retrieve enrichmentcommand does not yet supportApps -> STRING Enrichment -> Retrieve functional enrichmentequivalent - 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.