regulatory-genomics

Combined RNA and ATAC Footprint Training of Gene Regulatory Network

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

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

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.

One interface to nine genomic deep-learning oracles — variant effect prediction, calibrated per-track percentiles, and plain-English analysis through MCP.

Elucidating the Utility of Genomic Elements with Neural Nets

surrogate quantitative interpretability for deepnets

Robust and efficient analysis of single-cell perturbation studies

Genomic sequence preprocessing toolkit

A unified framework for discovering, analyzing, integrating, and visualizing regulatory motifs and transcription factor binding sites across bulk, single-cell, and long-read sequencing modalities.

Interpretable machine learning system for discovering hidden regulatory switches in non-coding DNA using ENCODE genomic data. Optimized for resource-constrained, reproducible research.

Data-driven design of context-specific regulatory elements

lsgkm+gkmexplain with regression functionality. Builds off kundajelab/lsgkm (which has gkmexplain), which in turn builds off Dongwon-Lee/lsgkm (the original lsgkm repo)

A set of tutorials for how to use all the tools in ML4GLand

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

Interpreting sequence-to-function machine learning models

Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric p-value of the overlap of features. It then calculates a permutation based empirical p-value and an FDR

Integrative framework combining TF footprinting with genome-wide association analyses to identify causal noncoding variants and elucidate their regulatory mechanisms in gene regulation

A curated list of regulatory genomics papers and resources.

NCypher — honest, context-specific triage of non-coding regulatory variants in paediatric DMG. Built with Claude: Life Sciences (Researcher track).