cisformer

Contents:

  • Concept
    • What Cisformer Does
    • Model Rationale
    • Interpreting ATAC-to-RNA Links
    • Species Support
  • Installation
    • Install Order
    • Recommended Runtime Environment
    • Verify the Installation
    • GPU and Distributed Training
    • Bedtools Requirement
  • Quick Start
    • 1. Generate Config Files
    • 2. Prepare Input Data
    • RNA-to-ATAC
      • Preprocess
      • Train
      • Predict
    • ATAC-to-RNA
      • Preprocess
      • Train
      • Predict
    • Link cCREs to Genes
    • Next Steps
  • Usage
    • Species
    • generate_default_config
      • accelerate_config.yaml
      • atac2rna_config.yaml
      • rna2atac_config.yaml
    • data_preprocess
      • ATAC-to-RNA log1p Handling
    • atac2rna_train
    • atac2rna_predict
    • atac2rna_link
    • rna2atac_train
    • rna2atac_predict
    • Recommended File Organization
  • Publishing to GitHub and PyPI
    • Prerequisites
    • Dry Run
    • Publish
    • TestPyPI
    • Useful Options
  • Release Notes
    • Version 1.1.0
      • Added
      • Changed
      • Upgrade Notes
    • Version 1.0.1 - 2025-05-14
cisformer
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