scbean

Scbean integrates a range of models for single-cell data analysis, including dimensionality reduction, remvoing batch effects, and transferring well-annotated cell type labels from scRNA-seq to scATAC-seq and spatial resoved transcriptomics. It is efficient and scalable for large-scale datasets.

Scbean will also provide more fundamental analyses for multi-modal data and spatial resoved transcriptomics in the future.

scbean Installation

• Installation

scbean Tutorial

• Tutorials for scbean–DAVAE
  • Integrating multiple scRNA-seq data
  • Integrating Visium data
• Tutorials for scbean–VIPCCA
  • Integrating multiple scRNA-seq data
  • Analysis of VIPCCA integrated result in R
  • scRNA-seq+scATAC-seq integration
• Tutorials for scbean–VIMCCA
  • Joint analyse of RNA + ATAC multimodal dataset using VIMCCA
  • Joint analyse of RNA + Protein multimodal dataset using VIMCCA
  • Joint analyse of RNA+ADT multimodal dataset using VIMCCA
• Tutorials for scbean–VISGP
  • Analyse of Spatial Transcriptome data using VISGP
  • Analysis of VISGP result in R
• Indices and tables

scbean API

• API
  • Preprocessing
  • Plotting
  • DAVAE
  • VIPCCA
  • VIMCCA
  • VISGP

Indices and tables

• Index

• Module Index

• Search Page