regulatory-genomics

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

Combined RNA and ATAC Footprint Training of Gene Regulatory Network

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

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.

Elucidating the Utility of Genomic Elements with Neural Nets

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

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.

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)

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

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

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

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

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).