Analyze the active regulatory region of DNA using FFNN and CNN

squid repository for manuscript analysis

Deep learning model for non-coding regulatory variants

Threshold and p-value computations for Position Weight Matrices

A curated list of regulatory genomics papers and resources.

Repository documenting applications of the ML4GLand suite on published datasets

Datasets for benchmarking, testing and developing in EUGENe

Prediction of transcription factor binding based on DNA sequence

Data-driven design of context-specific regulatory elements

A Hugo-based deployment of biocomputeobject.org

R package for plotting Islet Regulome data.

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

Motif representation and analysis toolkit in Python

Deep Unfolded Convolutional Dictionary Learning for motif discovery.

Genomic sequence preprocessing toolkit

Interpreting sequence-to-function machine learning models

surrogate quantitative interpretability for deepnets

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

Elucidating the Utility of Genomic Elements with Neural Nets

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