PhyloNetworks: a julia package with utilities for phylogenetic networks
Repository Index
47,133 repositories indexed
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Open-source software for exploring and analyzing large, high-dimensional image-derived data.
- cellprofiler-analyst
- cellprofiler
- image-analysis
- machine-learning
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
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
Integrated pipeline for multiplexed image analysis
- multiplexed-imaging
- python
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
Toolbox for the analysis of smFISH images.
- pattern-classification
- rna-localization
- segmentation
- smfish
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
Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
- cell-annotation
- multiplexed-imaging
- mpif
Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
- foundation-models
- gpt
- single-cell
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
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
scPair: Boosting single cell multimodal analysis by leveraging single cell atlases and implicit feature selection
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.
Analysis of cell migration in Igor Pro
- igor
- imagej
- cell-migration
- tracking
XitoSBML - the spatial SBML plugin for ImageJ
- sbml
- systems-biology
- spatial-sbml-plugin
- imagej
Vendor-agnostic, FHIR-Genomics-aligned API contract for cross-vendor NGS interpretation. JSON Schema + TypeScript + Python pydantic.