Single-Cell RNA-seq

Tutorials for the complete single-cell workflow: alignment, preprocessing, annotation, trajectory analysis, cell-structure analysis, velocity, and multi-omics.

• Alignment
  • Alignment and analysis of single-cell RNA-seq data
  • Alignment and RNA velocity analysis of single-cell RNA-seq data.
• Preprocessing
  • Preprocessing the data of scRNA-seq with omicverse[CPU-GPU-mixed]
  • Preprocessing the data of scRNA-seq with omicverse[GPU]
  • Clustering space
  • Data integration and batch correction
  • GeneModule Identified
  • Lazy analysis of scRNA-seq
• Annotation
  • Reference-free automated single-cell cell type annotation
  • Reference automated single-cell cell type annotation
  • Automatic cell type annotation with GPT/Other
  • Mapping Cell Names to the Cell Ontology/Taxonomy
  • Celltype auto annotation with SCSA
  • Celltype auto annotation with MetaTiME
  • Celltype annotation migration(mapping) with TOSICA
  • Using scMulan to annotate cell types in Heart, Lung, Liver, Bone marrow, Blood, Brain, and Thymus
  • 1. load h5ad
  • 2. transform original h5ad with uniformed genes (42117 genes)
  • 3. process uniformed data (simply norm and log1p)
  • 4. load scMulan
  • 5. visualization
  • Consensus annotation with CellVote
• Trajectory
  • Prediction of absolute developmental potential using CytoTrace2
  • Basic Trajectory Inference
  • Trajectory Inference with StaVIA
  • Timing-associated genes analysis with TimeFateKernel
  • Identify the driver regulators of cell fate decisions
  • Data loading and processing
  • Training CEFCON model
  • Downstream analysis
• Cell Structure
  • Inference of MetaCell from Single-Cell RNA-seq
  • Differential expression and celltype analysis [All Cell]
  • Differential expression analysis [Meta Cell]
  • Gene Regulatory Network Analysis with SCENIC
  • Pathway analysis with AUCell
  • Cell-cell communication using CellPhoneDBViz
  • Drug response predict with scDrug
  • Data integration and batch correction with SIMBA
• Velocity
  • Velocity Basic Calculation
  • Velocity Optimization
• Multi-omics
  • Multi omics analysis by MOFA
  • Multi omics analysis by MOFA and GLUE
  • Celltype annotation transfer in multi-omics