Tutorials

Examples data

Some processed files have been uploaded to Zenodo (DOI: https://doi.org/10.5281/zenodo.16959682) for direct use. Others can be obtained via the download links provided in this tutorial.

Major tutorials

• 1. Within-sample analysis
  • 1. Download data (mouse brain)
  • 2. Read and filter data
  • 3. Process scRNA-seq data to generate raw cell embeddings
  • 4. Training/test data prepare
  • 5. Train XChrom
  • 6. Evaluate the Model Performance
• 2. Cross-sample analysis
  • 1. Download Data (BMMCs: s1d1-s2d1)
  • 2. Read and filter data
  • 3. Process scRNA-seq data to generate raw cell embeddings (2 samples batch correction)
  • 4. Training/test data prepare
  • 5. Train XChrom
  • 6. Evaluate model performance in cross-sample scenario
• 3. Cross-species analysis
  • 1. Download Data (Human: m1d1, Mouse: mop3c2)
  • 2. Read and filter data
  • 3. Training/test data prepare
  • 4. Train XChrom
  • 5. Evaluate model performance in cross-species scenario
  • 6. Calculate ISM
  • 7. Calculate PWM-ISM dot product
• 4. COVID-19 analysis
  • 1. Download Data (PBMC10k, COVID-19)
  • 2. Training/test data prepare
  • 3. Train the model
  • 4. Calculate TF activity
  • 5. Check TF activity in different cell types
• 5. Pretrained XChrom
  • 1. Download data and pretrained model
  • 2. Map the new scRNA-seq sample to the reference RNA embedding space
  • 3. Predict chromatin accessibility for the new sample
  • 4. Evaluate the cell-state structure of predicted accessibility
  • 5. Calculate transcription factor activity