Repository Index

Code for the ProteinMPNN paper

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

• workflow-execution
• workflow
• cloud
• hpc

Cloud-native genomic dataframes and batch computing

• genetics
• vcf
• genomics
• gwas

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

Official repository for the ProteinGym benchmarks

• benchmark
• computational-biology
• protein
• protein-design

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

• bioinformatics
• taxonomy
• cross-platform
• lineage

Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk

• bioinformatics
• exact-optimization
• metabolomics
• paired-data

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

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising

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

Interpretable bilinear attention network with domain adaptation improves drug-target prediction.

Data visualisation web components for the life sciences.

• biohackeu21
• bioinformatics
• visualization
• webcomponents

GeneCompass

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

• computational-biology
• bioinformatics
• graph-convolution
• deep-learning

PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).

• deep-generative-model
• deep-learning
• single-cell-data-integration
• single-cell-multiomics

Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications

• cell-annotation
• multiplexed-imaging
• mpif

Tool for precise, interactive, fast and scalable FISH spot detection

MCP server for spatial transcriptomics analysis through natural language interfaces.

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

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

• bioinformatics
• cell-type-deconvolution
• computational-biology
• deconvolution

PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"

Official implementation of JAMIE, Joint variational Autoencoders for Multimodal Imputation and Embedding

• autoencoder
• imputation
• integration
• multimodal