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Rewrite ContextNet tutorials: runnable, reproducible, biologically framed #2

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Huangy57 merged 3 commits into from
May 20, 2026
Merged

Rewrite ContextNet tutorials: runnable, reproducible, biologically framed #2

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e6e8daf
Make tutorials runnable and reproducible: portable kernel, local-data…
Huangy57 May 20, 2026
cfffd01
Tutorials: apply review #27 nice-to-haves (cosmetic/prose polish)
Huangy57 May 20, 2026
cf45ee1
Merge branch 'main' into huangy57/contextnet-tutorials
Huangy57 May 20, 2026
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4 changes: 3 additions & 1 deletion README.md
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Expand Up @@ -95,7 +95,7 @@ ligand_activities(result)

### Sankey visualization with ccflowR

ContextNet pairs with [ccflowR](https://github.com/settylab/ccflowR) to render cell-cell communication as a Sankey diagram (sender → ligand → receptor → target → receiver).
ContextNet pairs with [ccflowR](https://github.com/settylab/ccflowR) to render cell-cell communication as a Sankey diagram (sender → ligand → receptor → target → receiver). ccflowR is an **optional** dependency: `prepare_for_ccflowr()` + `combine_sankey_data()` build the Sankey data table from base ContextNet, and only `sankey_flow()` requires ccflowR. The tutorials run end to end without it.

```r
library(ccflowR)
Expand All @@ -119,6 +119,8 @@ sankey_flow(sankey_data, cell_colors)
| [02 - Standard Workflow](notebooks/02-standard-workflow.ipynb) | Full NicheNet workflow with Sankey visualization |
| [03 - Multi-Condition Workflow](notebooks/03-multicondition-workflow.ipynb) | Differential analysis with MultiNicheNet and biological replicates |

These are full local-data tutorials: they read a context-specific GRN, a Seurat object, and the NicheNet priors from a local `data/` directory and do not download anything while running. See [notebooks/README.md](notebooks/README.md) for data requirements, kernel setup, and an example-data strategy.

## Key Functions

### GRN Import
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