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
Repository Index
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OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
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
OCaml Bioinformatics Library
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
PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.
The repository host gives no description.
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
BulkFormer: A large-scale foundation model for human bulk transcriptomes
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
- r
- neuroanatomy-toolbox
- cran
- neuron
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
- cell-annotation
- multiplexed-imaging
- mpif
The framework for quantification of neuronal anatomy
- neuroscience
- neuroanatomy-toolbox
- imagej
- imagej2
High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
Tool for precise, interactive, fast and scalable FISH spot detection
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
- single-cell
- scrna-seq
- scatac-seq
- deep-neural-networks
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
Predicting Cell Health with Morphological Profiles
- carpenter-lab
- morphological-profiling
- crispr
- cell-painting
CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
- cancer
- foundation-model
- single-cell