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

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

• pytorch
• protein-structure
• alphafold2

Chai-1, SOTA model for biomolecular structure prediction

Cloud-native genomic dataframes and batch computing

• genetics
• vcf
• genomics
• gwas

Precision Medicine Knowledge Graph (PrimeKG)

• knowledge-graph
• precision-medicine
• therapeutics
• bioinformatics

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

• foundation-models
• genomics
• language-models

A Go package for engineering organisms.

• synthetic-biology
• synbio
• genetic-engineering
• molecular-biology

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

• variant-calling
• genomics
• vcf-manipulation
• genotyping

Fast, sensitive and accurate integration of single-cell data with Harmony

• scrna-seq
• algorithm
• data-integration
• r

A dependency-free cross-platform swiss army knife for PDB files.

• python
• protein
• pdb
• bioinformatics

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

• cancer-genomics
• cnv-detection
• single-cell
• phylogeny

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

LLM for Drug Editing, ICLR 2024

• chatgpt
• conversation
• drug
• drug-discovery

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

Data visualisation web components for the life sciences.

• biohackeu21
• bioinformatics
• visualization
• webcomponents

Structural variant detection and association testing

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations

The repository host gives no description.

MCP server for spatial transcriptomics analysis through natural language interfaces.

• bioinformatics
• cell-communication
• deconvolution
• machine-learning

3D shape analysis using deep learning

• cancer-biology
• cell-biology
• deep-learning
• geometric-deep-learning

DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.