Biological foundation modeling from molecular to genome scale
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🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
- ai-agents
- bioinformatics
- equity
- genomics
An open-source application for biological image analysis
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
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
A tool for semi-automatic cell type classification
- python
- single-cell
- machine-learning
- scrna-seq
RNA Velocity generalized through dynamical modeling
Sequential regulatory activity predictions with deep convolutional neural networks.
The repository host gives no description.
Schema and generated objects for biolink data model and upper ontology
- biolink
- monarchinitiative
- gene-ontology
- datamodel
RNA-seq prediction with deep convolutional neural networks.
Bi-Directional Equivariant Long-Range DNA Sequence Modeling
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.
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
OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph 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
The repository host gives no description.
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
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
TypeDB Bio: Biomedical Knowledge Graph
- bioinformatics
- knowledge-graph
- knowledge-base
- drug-discovery
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics