Regulatory Genomics Python Packages

crested

CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

fp-tools-bio

Command-first ATAC-seq footprinting, motif analysis, and reproducible interactive reports

tfbs-footprinting

Pipeline: Identification of cis-regulatory elements by matrix scoring and conservation.

tfbs-footprinting3

Pipeline: Identification of cis-regulatory elements by matrix scoring and analysis of supporting empirical biological data.

dnadiffusion

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨