Ocelli

Ocelli is a lightweight Python package for scalable visualization and exploration of developmental multimodal single-cell data.

Ocelli (singular Ocellus, Latin: little eye) – simple eyes found in many insects in triplets. Their function is to navigate insects during the day or to detect movement.

The source code is available on GitHub.

Tutorials

• Welcome to Ocelli!
• Tutorial 1: Simulated data
  • Simulated data I: A binary tree
    • Exploring single modalities
    • Multimodal Diffusion Maps (MDM)
    • Visualizing MDM components
    • Interpreting multimodal weights
    • The advantage of multiple modalities
  • Simulated data II: Rare transitions
    • Exploring single modalitites
    • Multimodal Diffusion Maps
    • Visualizing MDM components
    • Multimodal weights distribution
• Tutorial 2: Hair follicle (ATAC-seq + RNA-seq)
  • Loading and preprocessing data
  • Multimodal Diffusion Maps
  • Visualizing MDM components with RNA velocity
  • Interpreting multimodal weights
  • Analyzing gene signatures
    • Hair shaft (HS) gene signatures
    • Inner root sheath (IRS) gene signatures
• Tutorial 3: Diffusion-based multimodal imputation
  • Loading and preprocessing data
  • Multimodal Diffusion Maps
  • Imputation of RNA-seq gene expression
  • Imputation of ATAC-seq peak activity
• Tutorial 4: Human bone marrow (ATAC-seq + Protein Epitopes)
  • Loading and preprocessing data
  • Multimodal Diffusion Maps
  • Visualizing MDM components
  • Interpreting multimodal weights
  • Investigating protein marker levels
    • CD14 (CD14+ Monocytes)
    • CD71 (Erythroid cells)
    • CD34 (Hematopoietic stem cells)
    • CD123 (Plasmacytoid dendritic cells)
    • CD19 (B cells)
    • CD4 (CD4+ naive T cells)
    • CD8 (CD8+ naive T cells)
• Tutorial 5: Diffusion-based multimodal exploration of subtrajectories
  • Loading data
  • Multimodal Diffusion Maps
  • Multimodal diffusion of hematopoietic stem cells
  • Finding subtrajectories around HSCs
• Tutorial 6: Exploring unimodal data
  • Pancreatic endocrinogenesis (RNA-seq)
    • Loading and preprocessing data
    • Multimodal Diffusion Maps
    • Visualizing MDM components
    • Reconstructing the cell cycle of Ductal cells
    • Tracing the development of endocrine cells
  • iPSCs reprogramming (RNA-seq)
    • Loading and preprocessing data
    • Multimodal Diffusion Maps
    • Visualizing MDM components with Waddington Optimal Transport
    • Tracing the developmental ancestors of iPSCs
    • Sensitivity to rare cell populations