zebrafish embryogenesis - case study

Danio rerio embryogenesis single-cell data analysis example

Please download the notebooks from here . Or please click below to view the content.

• Case study: re-analysis of zebrafish (Danio rerio) embryogenesis single-cell data
  • Notebook file
  • Steps
  • Import libraries
  • Import oggmap python package submodules
  • Step 0 - run OrthoFinder to obtain orthogroups
  • Step 1 - get query species taxonomic lineage information
  • Step 2 - gene age class assignment (query species orthomap)
    • Gene age assignments per query species lineage node
    • Visualize number of species along query lineage and counts per gene age class
  • Step 3 - map OrthoFinder gene names and scRNA gene/transcript names
    • Import now, the scRNA dataset of the query species
    • Get an overview of observations
    • Helper functions to match gene names
    • Reduce isoforms to genes
  • Step 4 - get TEI values and add them to scRNA dataset
    • add TEI to adata object
  • Step 5 - downstream analysis
    • Boxplot gene age class per embryo stage
    • Boxplot gene age class per embryo stage and add significance
    • Boxplot gene age class per embryo stage and per cell type
    • Plot relative expression per gene age class per sample stage
    • Get partial TEI values to visualize gene age class contributions
    • Gene age class contribution of one cell type
    • Color UMAP/TSNE by TEI
      • Filtering
      • Normalization, Log transformation and Scaling
      • PCA and Neighbor calculations
      • Embedding the neighborhood graph
      • UMAP