Tutorials

Using transmorph within a scanpy pipeline

• Setting up transmorph within a scanpy workflow
  • Datasets presentation
  • Dataset integration
  • Label transfer

Presenting the pre-built models

• Joint embedding of annotated osteosarcoma datasets using EmbedMNN model
  • Loading the data bank
  • Plotting initial datasets with scatter_plot
  • Assessing mixing using LISI
  • Dataset integration using EmbedMNN
  • Integration analysis with LISI
• Unsupervised integration of nasopharyngal carcinoma datasets using EmbedMNN model
  • Loading the data bank
  • Plotting initial datasets with scatter_plot
  • Dataset integration using EmbedMNN
  • Integration analysis with LISI
• Correcting counts in nasopharyngal carcinoma datasets using MNNCorrection model
  • Loading the data bank
  • Plotting initial datasets
  • Dataset integration using MNNCorrection
  • Integration analysis with LISI
• Transferring cell cycle annotation using TransportCorrection
  • Loading datasets
  • Observing cell cycle
  • Performing integration and label transfer

Building models with the model API

• Creating a custom data integration model
  • Model architecture
  • Recreating the EmbedMNN model using the model API
  • Testing this model on a single-cell dataset
• A tour of transmorph transformation modules
  • Test dataset and model
  • Common features reduction
  • Principal component analysis
  • Independent component analysis
  • Neighborhood-based pooling
  • Creating a custom transformation module
• A tour of transmorph matching modules
  • Toy dataset and plotting function
  • Label-based matching
  • Batch \(k\)-nearest neighbors matching
  • Mutual nearest neighbors matching
  • Discrete transportation-based matchings
  • Creating a custom matching module
• A tour of transmorph merging modules
  • Toy dataset and plotting function
  • Barycentric merging
  • Linear correction merging
  • Graph embedding merging
  • Implementing a custom merging