Popular GitHub Repositories for Regulatory Genomics

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A collaboratively written review paper on deep learning, genomics, and precision medicine

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

Using an LLM to discover the genetic causes of rare disease

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

? Generative modeling of regulatory DNA sequences with diffusion probabilistic models ?

Single cell perturbation prediction

Genomic Pre-trained Network

✨ ML/AI, Medicine, Genomics, Science Research

Ten Quick Tips for Deep Learning in Biology

Training and evaluating a variational autoencoder for pan-cancer gene expression data

生物医学模型上下文协议

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

Easy genetic ancestry predictions in Python

My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other hierarchical methods)

Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.

Deep Motif (ICLR16)/ Deep Motif Dashboard (PSB17): Visualizing Genomic Sequence Classifications

This is a python package for genomics study with a GCN framework.

Mandrake ?/???? – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Proof of concept code from Gretel.ai and Illumina using generative neural networks to create synthetic versions of mouse genotype and phenotype data.