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]
  • Preprocessing the data of scRNA-seq [Rust / out-of-memory]
  • 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
  • Consensus annotation with CellVote — PBMC3k
  • Mapping Cell Names to the Cell Ontology/Taxonomy
  • Individual methods
• MetaCell
  • MetaCell
  • Recommended workflow: SEACells end-to-end + downstream sanity
  • Multi-sample metacells with batch correction
  • MetaCell zoo
  • SEACells — kernel archetypal analysis
  • MetaQ — VQ-VAE codebook metacells
  • SuperCell — kNN graph + walktrap community detection
  • k-means — the trivial baseline that’s often hard to beat
  • random — the honest lower-bound baseline
  • GeoSketch — density-aware sketching as a metacell baseline
  • Side-by-side comparison of all metacell backends
• Trajectory
  • Prediction of absolute developmental potential using CytoTrace2
  • Trajectory Inference with Diffusion Map and PAGA
  • Trajectory Inference with Slingshot
  • Trajectory Inference with Palantir
  • Trajectory Inference with scTour
  • Trajectory Inference with Monocle 2 on the Olsson Hematopoiesis Dataset
  • Trajectory Inference with StaVIA
  • Trajectory Inference with VIA and scVelo
  • Timing-associated genes analysis with TimeFateKernel
  • Identify the driver regulators of cell fate decisions
  • Data loading and processing
  • Training CEFCON model
  • Downstream analysis
• Cell-Cell Communication
  • Cell-cell communication analysis with CellPhoneDB
  • 1. ov.pl.ccc_heatmap
  • 2. ov.pl.ccc_network_plot
  • 3. ov.pl.ccc_stat_plot
  • Cell-cell communication analysis with LIANA+
  • 1. ov.pl.ccc_heatmap
  • 2. ov.pl.ccc_network_plot
  • 3. ov.pl.ccc_stat_plot
• Cell Structure
  • Differential expression and celltype analysis [All Cell]
  • Differential expression analysis [Meta Cell]
  • Gene Regulatory Network Analysis with SCENIC
  • Drug response predict with scDrug
  • Data integration and batch correction with SIMBA
• Copy-Number Variation
  • Single-cell copy-number variation with CopyKAT
  • Single-cell copy-number variation with inferCNV
• Enrichment
  • Pathway analysis with AUCell
  • Comparing enrichment-score methods on scRNA-seq
• Velocity
  • Velocity Basic Calculation
  • Velocity Optimization
  • Velocity-guided CellRank Analysis
• Multi-omics
  • Multi omics analysis by MOFA
  • Multi omics analysis by MOFA and GLUE
  • Celltype annotation transfer in multi-omics