Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
Repository Index
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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
- tensorflow
- deep-neural-network
- genomics
- science
Single-cell analysis in Python. Scales to >100M cells.
- machine-learning
- data-science
- visualize-data
- transcriptomics
Data intensive science for everyone.
Open source tools for computational pathology - Nature BME
- histopathology
- pathology
- weakly-supervised-learning
- whole-slide-imaging
🦖 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
Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
Interactive network visualization in Python and Dash, powered by Cytoscape.js
- plotly-dash
- plotly
- dash
- cytoscape
Vision-Language Pathology Foundation Model - Nature Medicine
- bioimage-analysis
- bioimage-informatics
- conch
- foundation-model
Graph-linked unified embedding for single-cell multi-omics data integration
- bioinformatics
- deep-learning
- single-cell
- single-cell-multiomics
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
AI-based pathology predicts origins for cancers of unknown primary - Nature
- histology
- pathology
- wsi-images
- histopathology
Open source tumor evidence matching for sequencing labs and hospitals without molecular tumor boards. Research prototype; oncologist review required.
- bioinformatics
- cancer-research
- computational-biology
- drug-repurposing
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
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
TypeDB Bio: Biomedical Knowledge Graph
- bioinformatics
- knowledge-graph
- knowledge-base
- drug-discovery
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
- computational-biology
- bioinformatics
- graph-convolution
- deep-learning
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources
- bioimage-analysis
- cell-classification
- computer-vision
- digital-pathology
Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics
- bioinformatics
- cell-type-deconvolution
- computational-biology
- deconvolution