Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
Repository Index
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Biomni: a general-purpose biomedical AI agent
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
- pytorch
- protein-structure
- alphafold2
NeuroKit2: The Python Toolbox for Neurophysiological Signal Processing
- python
- ecg
- eda
- emg
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
- ai-agents
- bioinformatics
- equity
- genomics
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
Sequential regulatory activity predictions with deep convolutional neural networks.
The repository host gives no description.
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
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.
Accurate and efficient spot detection for microscopy data
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
Toolbox for the analysis of smFISH images.
- pattern-classification
- rna-localization
- segmentation
- smfish
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
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
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
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
DeepAEG: A model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies