cisformer

Contents:

  • Conception
  • Installation Guide
    • Miniconda3
    • Creating the Cisformer Environment
    • Install from PyPI
  • Quick Start
    • Generate Default Config Files
    • RNA ➝ ATAC
      • 1. Configure Parameters (Optional)
      • 2. Preprocess Data
      • 3. Train the Model
      • 4. Run Prediction
    • ATAC ➝ RNA
      • 1. Configure Parameters (Optional)
      • 2. Preprocess Data
      • 3. Train the Model
      • 4. Run Prediction (Optional)
      • 5. Link Cis-Regulatory Elements to Genes
  • Usage
    • generate_default_config
      • accelerate_config.yaml
      • atac2rna_config.yaml
      • rna2atac_config.yaml
    • data_preprocess
    • atac2rna_train
    • atac2rna_predict
    • atac2rna_link
    • rna2atac_train
    • rna2atac_predict
  • Detailed Function Composition
    • cisformer package
      • Subpackages
        • cisformer.M2Mmodel package
      • Submodules
      • cisformer.atac2rna_predict module
      • cisformer.atac2rna_surround_attention_generate module
      • cisformer.atac2rna_train module
      • cisformer.compute_surround_enhancer module
      • cisformer.data_preprocess module
      • cisformer.generate_default_config module
        • main()
      • cisformer.map_rna_atac module
      • cisformer.rna2atac_predict module
      • cisformer.rna2atac_train module
      • cisformer.runner module
      • Module contents
  • Release notes
    • Version 1.0.1 2025-5-14
cisformer
  • Detailed Function Composition
  • View page source

Detailed Function Composition

  • cisformer package
    • Subpackages
      • cisformer.M2Mmodel package
        • Submodules
        • cisformer.M2Mmodel.M2M module
        • cisformer.M2Mmodel.block module
        • cisformer.M2Mmodel.utils module
        • Module contents
    • Submodules
    • cisformer.atac2rna_predict module
    • cisformer.atac2rna_surround_attention_generate module
    • cisformer.atac2rna_train module
    • cisformer.compute_surround_enhancer module
    • cisformer.data_preprocess module
    • cisformer.generate_default_config module
      • main()
    • cisformer.map_rna_atac module
    • cisformer.rna2atac_predict module
    • cisformer.rna2atac_train module
    • cisformer.runner module
    • Module contents
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