Tutorials

• Standard pipeline: analyzing 5K PBMC dataset from 10X genomics
  • Introduction
  • Import library and environment setup
  • Preprocessing
  • Dimension reduction
  • Clustering analysis
  • Cell cluster annotation
  • What’s next?
• Annotating cell clusters by integrating single-cell RNA-seq data
  • Introduction
  • Preparing data
  • Data integration
  • What’s next?
• Identify differentially accessible regions
  • Peak calling at the cluster-level
  • Finding marker regions
  • Regression-based differential test
• Multi-sample Pipeline: analyzing snATAC-seq data of human colon samples
  • Introduction
  • Creating AnnDataSet object
  • Batch correction
  • Clustering
  • Peak calling
  • AnnDataSet object IO
• Multi-modality pipeline: analyzing single-cell multiome data (ATAC + Gene Expression)
  • Introduction
  • Analyze gene expression data
  • Analyze chromatin accessibility data
  • Perform joint embedding
• Atlas-scale Analysis: a cell atlas of human chromatin accessibility.
  • Introduction
  • Preprocessing
  • Dimensionality reduction
  • Batch correction
  • Clustering
  • Visualization
  • Subclustering