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
cisformer package
cisformer.M2Mmodel package
View page source
cisformer.M2Mmodel package
Submodules
cisformer.M2Mmodel.M2M module
cisformer.M2Mmodel.block module
cisformer.M2Mmodel.utils module
Module contents