scCAMEL
Pip installation via: https://pypi.org/project/scCAMEL/
Developed by YZstudio (Karolinska Institutet, Sweden)
Github: https://github.com/StudioYZ
Technical support from: Ernfors Lab (Karolinska Institutet, Sweden)
Content:
Contents:
- Installation
- Tutorials_scCAMEL_SWAPLINEv2
- Tutorials_scCAMEL-SWAPLINE_SensoryNeurons_Training-SharmaMouse_Predict_ZeiselMouse
- Training
- Prefiltering_and_SelectFeatures
- Neural-Network learning
- Accuracy plot, the overall clustering accuracy is ~85%
- Make predition and visualization in Radar plot
- permutation control
- Cluster consistency and accuracy
- Cell_Type Purity
- association between cell-types
- Save data
- Prediction
- ZeiselMouse_cluster
- Save data
- Tutorial: scCAMEL-SWAPLINE Mouse Dentate Gyrus to Human Glioblastoma
- Training
- Prefiltering_and_SelectFeatures
- Neural-Network learning
- Accuracy plot, the overall clustering accuracy is ~95%
- Save and Reload the Trained Model
- Make predition and visualization in Radar plot
- permutation control
- Cell_Type Purity
- association between cell-types
- Save data
- Prediction
- Couturier2020_humanGlioblastoma
- Save data
- Tutorials_scCAMEL-SWAPLINEv1_LiverMacrophage
- Tutorials_scCAMEL-SWAPLINE_SensoryNeurons_Training-SharmaMouse_Predict_ZeiselMouse
- Tutorials_scCAMEL_EVO
- Tutorials_scCAMEL_VICUNA
- Tutorial: VICUNA intercellular communication with PyPI scCAMEL 0.47b1
- 1. Configure paths and import PyPI scCAMEL
- 2. Load datasets and humanize mouse genes
- 3. Select NTN1 ligand-receptor pairs
- 4. Compute sparse VICUNA EScore matrices
- 5. Score cross-dataset NTN1 communication
- 6. Build tidy result tables
- 7. Plot NTN1 ligand activity
- 8. Plot cluster-pair communication heatmaps
- 9. Plot receptor-by-target heatmaps
- 10. Plot top NTN1 ligand-receptor interactions
- 11. Chord-style cluster communication plot
- 12. Sankey/alluvial plot for top paths
- 13. Review key results and generated files
- Tutorial: VICUNA intercellular communication with PyPI scCAMEL 0.47b1
- scCAMEL_ALPACA
- Datasets_Visualizations
- Reference