Tutorials for scbean–DAVAE

• Integrating multiple scRNA-seq data
  • Importing scbean package
  • Loading data
  • Data preprocessing
  • DAVAE Integration
  • UMAP Visualization
• Integrating Visium data
  • Importing scbean package
  • Loading data
  • Data preprocessing
  • DAVAE integration
  • UMAP visualization and clustering
  • Visualization in spatial coordinates
  • Import additional package
  • Loading data
  • Preprocessing
  • DAVAE integration
  • Calculate distance
  • Transfer label
  • Visualize the neurons cortical layers

Tutorials for scbean–VIPCCA

• Integrating multiple scRNA-seq data
  • Importing scbean package
  • Loading data
  • Data preprocessing
  • VIPCCA Integration
  • Loading result
  • UMAP Visualization
  • Plot correlation
• Analysis of VIPCCA integrated result in R
  • Required packages
  • Read h5ad file with R
  • Calculating kBET
  • Differential gene analyses
  • Plotting Enhanced Volcano
• scRNA-seq+scATAC-seq integration
  • Preprocessing with R
  • Importing scbean package
  • Loading data in python
  • Data preprocessing
  • VIPCCA Integration
  • Cell type prediction
  • Loading result
  • UMAP Visualization

Tutorials for scbean–VIMCCA

• Joint analyse of RNA + ATAC multimodal dataset using VIMCCA
  • Import packages
  • Loading dataset
  • Preprocessing using scanpy
  • Joint analyse using VIMCCA
  • Visualization
• Joint analyse of RNA + Protein multimodal dataset using VIMCCA
  • Import packages
  • Loading dataset
  • Preprocessing using scanpy
  • Joint analyse using VIMCCA
  • Visualization
• Joint analyse of RNA+ADT multimodal dataset using VIMCCA
  • import packages
  • loading dataset
  • Processing with scanpy
  • Joint analyse using VIMCCA
  • Visualization

Tutorials for scbean–VISGP

• Analyse of Spatial Transcriptome data using VISGP
  • Import packages
  • Loading dataset
  • Preprocessing
  • Identify SV genes via VGP
• Analysis of VISGP result in R

Indices and tables

• Index

• Module Index

• Search Page