bio-spatial-transcriptomics-spatial-neighbors
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downstream spatial analyses. Use when building spatial neighborhood graphs.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-neighbors --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: matplotlib 3.8+, numpy 1.26+, scanpy 1.10+, scikit-learn 1.4+, scipy 1.12+, squidpy 1.3+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Spatial Neighbor Graphs **"Build a spatial neighborhood graph"** → Construct spatial connectivity graphs using k-nearest neighbors, Delaunay triangulation, or radius-based methods for downstream spatial statistics. - Python: `squidpy.gr.spatial_neighbors(adata, coord_type='generic', n_neighs=6)` Build spatial neighbor graphs for connectivity-based analyses. ## Required Imports ```python import squidpy as sq import scanpy as sc import numpy as np ``` ## Build K-Nearest Neighbors Graph **Goal:** Construct a spatial KNN graph connecting each spot to its nearest spatial neighbors. **Approach:** Use Squidpy's `spatial_neighbors` with k-nearest neighbors on coordinate distances. ```python # Build spatial KNN graph sq.gr.spatial_
- Version Compatibility
- Required Imports
- Build K-Nearest Neighbors Graph
- Build Delaunay Triangulation Graph
- Radius-Based Neighbors
- For Visium Data (Grid Structure)
- Access Neighbor Information
- Get Neighbors for a Specific Spot
- Build Expression-Based Neighbors
- Combine Spatial and Expression Neighbors
- Visualize Neighbor Graph
- Compute Graph Statistics
- Store Multiple Neighbor Graphs
- Related Skills
What does the bio-spatial-transcriptomics-spatial-neighbors skill do?
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downstream spatial analyses. Use when building spatial neighborhood graphs.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-neighbors --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.