Open-source software for exploring and analyzing large, high-dimensional image-derived data.
- cellprofiler-analyst
- cellprofiler
- image-analysis
- machine-learning
Repository Index
71,372 visible repositories in the index
49–72 of 77 · Most stars
LLM for Drug Editing, ICLR 2024
- chatgpt
- conversation
- drug
- drug-discovery
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.
Data visualisation web components for the life sciences.
- biohackeu21
- bioinformatics
- visualization
- webcomponents
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
OCaml Bioinformatics Library
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
Integrated pipeline for multiplexed image analysis
- multiplexed-imaging
- python
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
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
- computational-biology
- bioinformatics
- graph-convolution
- deep-learning
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
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
- epigenomics
- pattern-search
- data-visualization
- interactive-machine-learning
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
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
Methods for Image-Based Cell Profiling
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
Single-cell fluorescence microscopy data analysis
- microscopy
- fluorescence-microscopy-imaging
Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics
- bioinformatics
- cell-type-deconvolution
- computational-biology
- deconvolution
DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.