Repository Index

Open source code for AlphaFold 2.

AlphaFold 3 inference pipeline.

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

• drug-discovery
• quantum-chemistry
• deep-learning
• biology

Official repository for the Boltz biomolecular interaction models

• binding-prediction
• drug-discovery
• protein-structure

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

• tensorflow
• deep-neural-network
• genomics
• science

Code for running RFdiffusion

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues

• openworm
• elegans
• biology
• simulation

This package contains deep learning models and related scripts for RoseTTAFold

This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.

Chai-1, SOTA model for biomolecular structure prediction

Deep probabilistic analysis of single-cell and spatial omics data

• scrna-seq
• variational-bayes
• variational-autoencoder
• cite-seq

Biological foundation modeling from molecular to genome scale

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Python package for graph neural networks in chemistry and biology

• deep-learning
• graph-neural-networks
• dgl
• cheminformatics

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• dna
• k-mer
• python
• bloom-filter

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

Official release of the ProGen models

• language-model
• protein
• generative-model

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

OmegaFold Release Code

Generative biopolymer design with rich conditioning.

RNA Velocity generalized through dynamical modeling

Graph-linked unified embedding for single-cell multi-omics data integration

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

Sequential regulatory activity predictions with deep convolutional neural networks.