Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
Repository Index
47,133 repositories indexed
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Official repository for the Boltz biomolecular interaction models
- binding-prediction
- drug-discovery
- protein-structure
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
- pytorch
- protein-structure
- alphafold2
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
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
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
Official repository for the ProteinGym benchmarks
- benchmark
- computational-biology
- protein
- protein-design
Sequential regulatory activity predictions with deep convolutional neural networks.
Multi-Omics Factor Analysis
- multi-omics
- factor-analysis
- mofa
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
Schema and generated objects for biolink data model and upper ontology
- biolink
- monarchinitiative
- gene-ontology
- datamodel
Genomic sequence storage, indexing and alignment inside PostgreSQL: https://bioseqdb.com/
- alignment
- bioinformatics
- biology
- database
Repository for Nicheformer: a foundation model for single-cell and spatial omics
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
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
Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
- foundation-models
- gpt
- single-cell
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"