Welcome to the documentation of the single cell framework!

Contents:

• Changelog
  • 0.12.0 (19-12-24)
  • 0.11.0 (08-11-24)
  • 0.10.1 (17-09-24)
  • 0.10.0 (10-09-24)
  • 0.9.0 (02-08-24)
  • 0.8.0 (14-06-24)
  • 0.7.0 (23-04-24)
  • 0.6.1 (28-03-24)
  • 0.6 (27-03-24)
  • 0.5 (04-03-24)
  • 0.4 (31-1-24)
  • 0.3 (30-11-2023)
  • 0.2 (30-08-2023)
  • 0.1.1 (24-05-2023)
  • 0.1 (22-05-2023)
• RNA notebooks
  • 01 - Assembling or loading anndata object
  • 02 - QC and filtering
  • 03 - Normalization and Batch effect correction
  • 04 - Embedding and clustering
  • 0A - Receptor-Ligand Analysis
  • 0B - Velocity Analysis
• ATAC notebooks
  • 01 - Assembling or loading anndata object
  • 02 - QC and filtering
  • 03 - Normalization and Batch effect correction
  • 04 - Embedding and clustering
• General notebooks
  • Gene Set Enrichment Analysis (GSEA)
  • Cell type annotation and marker list assembly
  • Marker computation and analysis
  • Preparing adata for cellxgene / MaMPlan creation
  • Proportion Analysis
  • Trajectory and Pseudotime Analysis
• sctoolbox API reference
  • Tools
  • Plotting
  • Utils