nematode embryogenesis - case study

Caenorhabditis elegans 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 nematode (Caenorhabditis elegans) embryogenesis single-cell data
  • Notebook file
  • Steps
  • Import libraries
  • Import oggmap python package submodules
  • Step 0 - Use pre-calculated gene age classification
  • Step 0 - Use different pre-calculated evolutionary indices
  • Step 1 - get query species taxonomic lineage information
  • Step 2 - gene age class assignment (query species orthomap)
    • Get query species evolutionary indices
    • Group evolutionary indices into bins
    • Gene age assignments per query species lineage node
      • Gene assignments per query species evolutionary index
  • 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
  • step 4 - Get TEI values and add them to scRNA dataset
    • add TEI to adata object
    • add TajimaD, Fst and NormalizedPi to adata object
  • Step 5 - downstream analysis
    • Boxplot gene age class per sample timepoint
    • Boxplot TajimaD class per sample timepoint
    • Boxplot Fst class per sample timepoint
    • Boxplot NormalizedPi class per sample timepoint
    • Boxplot gene age class per sample timepoint and add significance
    • Boxplot gene age class per sample timepoint and per cell type
    • Scatterplot TEI vs TajimaD and color each cell by sample timepoint per cell type
    • Scatterplot TEI vs Fst and color each cell by sample timepoint per cell type
    • Scatterplot TEI vs NormalizedPi and color each cell by sample timepoint per cell type
    • Plot relative expression per gene age class per sample timepoint
    • Get partial TEI values to visualize gene age class contributions
      • partial TajimaD
      • partial Fst
      • partial NormalizedPi
    • Color UMAP/TSNE by TEI
      • Filtering
      • Normalization, Log transformation and Scaling
      • PCA and Neighbor calculations
      • Embedding the neighborhood graph
      • UMAP
      • Color UMAP by cell type
      • Color UMAP by TEI
      • Color UMAP by TajimaD bins
      • Color UMAP by Fst bins
      • Color UMAP by NormalizedPi bins
      • 3D-UMAP