Tutorials

• Manifold Fitting and Clustering
  • Data Reading
  • Normalization
  • Manifold Fitting Step 1
  • Manifold Fitting Step 2
  • Manifold Embedding in Graph and Clustering
  • Calculate the Clustering Accuracy (ACC,NMI,ARI,F1-Score,JI)
  • Visualization
• Tree Structure Construction
  • Hierarchical Clustering of the Data
  • Tree Structure Visualization
  • Marker Gene Between Each clusters
• Gene Analysis Through Different Layer
  • Retrieve the hierarchical structure of the data
  • Define the hierarchical structure to be considered
  • Calculate the Wasserstein distance between nodes at the same layer
  • Count the number of each gene type at each layer.
• Visualization on Marker Gene
  • Hierarchical Clustering of the Data
  • Identify the marker genes for Cluster 3-1 and Cluster 3-2
  • Color the visualization results using the expression levels of the marker genes
  • Plot the mean expression heatmap of genes across different cell groups
  • Plot the expression heatmap of marker genes across different cell types
  • Plot violin plots to compare the expression levels of marker genes between different classes
• Analysis of Disease-Control Cell Atlas
  • Run CellScope on the Dataset
  • CellScope has the ability to identify cell types.
  • Visualization on This System
  • The identification of marker genes for COVID-19 in the system.
  • Tree Structured of PBMC