Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
Repository Index
47,133 repositories indexed
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Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
- diffusion-models
- docking
- binding
- computational-biology
Brian is a free, open source simulator for spiking neural networks.
- python
- neuroscience
- science
- differential-equations
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
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
Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)
FiPy is a Finite Volume PDE solver written in Python
- scientific-computing
- scientific-computing-with-python
- phase-field
- materials-science
Spatial Single Cell Analysis in Python
- single-cell-rna-seq
- single-cell-genomics
- spatial-transcriptomics
- spatial-analysis
A Euclidean diffusion model for structure-based drug design.
- ddpm
- drug-design
- equivariance
- generative-model
A tool for semi-automatic cell type classification
- python
- single-cell
- machine-learning
- scrna-seq
Sequential regulatory activity predictions with deep convolutional neural networks.
A High-Level Abstraction Framework for Quantum Algorithms
Quantum Computer Library for Everyone
- quantum
- python
- quantum-computing
- quantum-algorithms
The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)
- ai-for-science
- diffusion-models
- drug-design
- equivariant-networks
RNA-seq prediction with deep convolutional neural networks.
Bi-Directional Equivariant Long-Range DNA Sequence Modeling
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
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
Autonomous multi-agent framework to optimize scientific software
- acceleration
- agentic-ai
- ai-agents
- bioinformatics