Repository Index

Official git repository for Biopython (originally converted from CVS)

• python
• bioinformatics
• genomics
• biopython

Deep probabilistic analysis of single-cell and spatial omics data

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

🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.

• ai-agents
• bioinformatics
• equity
• genomics

Cloud-native genomic dataframes and batch computing

• genetics
• vcf
• genomics
• gwas

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

Generative biopolymer design with rich conditioning.

RNA Velocity generalized through dynamical modeling

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

UCE is a zero-shot foundation model for single-cell gene expression data

Schema and generated objects for biolink data model and upper ontology

• biolink
• monarchinitiative
• gene-ontology
• datamodel

OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.

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

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

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

GNN-based gene-selection deep learning model for drug response prediction