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3. Gene-distance correlation
🎯 Goal: Link gene expression and distance to a structure.
We tested ERBB2 expression vs distance to the tumor margin.
🔵 Inside the tumor = negative distance
🔴 Outside = positive
➡️ ERBB2 expression drops as distance increases — just as expected.
🎯 Goal: Link gene expression and distance to a structure.
We tested ERBB2 expression vs distance to the tumor margin.
🔵 Inside the tumor = negative distance
🔴 Outside = positive
➡️ ERBB2 expression drops as distance increases — just as expected.
April 11, 2025 at 4:09 PM
3. Gene-distance correlation
🎯 Goal: Link gene expression and distance to a structure.
We tested ERBB2 expression vs distance to the tumor margin.
🔵 Inside the tumor = negative distance
🔴 Outside = positive
➡️ ERBB2 expression drops as distance increases — just as expected.
🎯 Goal: Link gene expression and distance to a structure.
We tested ERBB2 expression vs distance to the tumor margin.
🔵 Inside the tumor = negative distance
🔴 Outside = positive
➡️ ERBB2 expression drops as distance increases — just as expected.
2. Neighborhood analysis
🎯 Goal: See if clusters co-occur in space or avoid each other.
✅ Immune cells (cluster 4) are enriched (z-score>0) near tumor cells (cluster 1).
Why does this matter? It can drive downstream analyses like cell-to-cell communication between clusters.
🎯 Goal: See if clusters co-occur in space or avoid each other.
✅ Immune cells (cluster 4) are enriched (z-score>0) near tumor cells (cluster 1).
Why does this matter? It can drive downstream analyses like cell-to-cell communication between clusters.
April 11, 2025 at 4:09 PM
2. Neighborhood analysis
🎯 Goal: See if clusters co-occur in space or avoid each other.
✅ Immune cells (cluster 4) are enriched (z-score>0) near tumor cells (cluster 1).
Why does this matter? It can drive downstream analyses like cell-to-cell communication between clusters.
🎯 Goal: See if clusters co-occur in space or avoid each other.
✅ Immune cells (cluster 4) are enriched (z-score>0) near tumor cells (cluster 1).
Why does this matter? It can drive downstream analyses like cell-to-cell communication between clusters.
1. Spatial clustering
🎯 Goal: Find regions with distinct gene expression and spatial coherence.
✅ In a HER2+ breast cancer sample, spatial-aware clustering found immune cells (green) around the tumor, just like the pathologist said.
❌ Expression-only clustering missed it.
🎯 Goal: Find regions with distinct gene expression and spatial coherence.
✅ In a HER2+ breast cancer sample, spatial-aware clustering found immune cells (green) around the tumor, just like the pathologist said.
❌ Expression-only clustering missed it.
April 11, 2025 at 4:09 PM
1. Spatial clustering
🎯 Goal: Find regions with distinct gene expression and spatial coherence.
✅ In a HER2+ breast cancer sample, spatial-aware clustering found immune cells (green) around the tumor, just like the pathologist said.
❌ Expression-only clustering missed it.
🎯 Goal: Find regions with distinct gene expression and spatial coherence.
✅ In a HER2+ breast cancer sample, spatial-aware clustering found immune cells (green) around the tumor, just like the pathologist said.
❌ Expression-only clustering missed it.
How to squeeze your spatial transcriptomics data? 🍋
Some scientists claim spatial transcriptomics (ST) will replace single-cell technologies. Others say it's just a pricier single-cell with a nice visual output. So...who's right?
A thread on #SpatialTranscriptomics ⬇️
Some scientists claim spatial transcriptomics (ST) will replace single-cell technologies. Others say it's just a pricier single-cell with a nice visual output. So...who's right?
A thread on #SpatialTranscriptomics ⬇️
April 11, 2025 at 4:09 PM
How to squeeze your spatial transcriptomics data? 🍋
Some scientists claim spatial transcriptomics (ST) will replace single-cell technologies. Others say it's just a pricier single-cell with a nice visual output. So...who's right?
A thread on #SpatialTranscriptomics ⬇️
Some scientists claim spatial transcriptomics (ST) will replace single-cell technologies. Others say it's just a pricier single-cell with a nice visual output. So...who's right?
A thread on #SpatialTranscriptomics ⬇️