6  Single Cell

6.1 Packages

• R:
  • General analysis:
    • Seurat
  • Annotation:
    • sc-type
    • SingleR
  • Trajectories:
    • dynverse
    • monocle3
    • slingshot
  • Spatial analysis:
    • semla
• Python:
  • General analysis:
    • scanpy
    • anndata

6.2 Documentation

• Best practices in single cell [link]
• Tools developped for single cell [link]

6.3 Databases

• cellxgene
• Human Cell Atlas
• EBI Single Cell Expression Atlas
• Arc Virtual Cell Atlas: 230 million cells (and expanding), spanning 21 organisms and 72 tissues