Probabilistic cell segmentation for in situ spatial transcriptomics
Repository Index
70,234 visible repositories in the index
25–48 of 50 · Most stars
Repository for Nicheformer: a foundation model for single-cell and spatial omics
PhyloNetworks: a julia package with utilities for phylogenetic networks
The repository host gives no description.
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
Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
Structural variant detection and association testing
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
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
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
Run scripts, explore your genome, and get personalized explanations — all in natural dialogue.
- analysis
- claude
- claudecode
- dna
Tool for precise, interactive, fast and scalable FISH spot detection
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
Deciphering cell-cell communication from spatially resolved transcriptomic data at single-cell resolution with subgraph-based attentional graph neural network
A versatile single-cell cross-modality translation method via dual-aligned variational autoencoders
Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics
- bioinformatics
- cell-type-deconvolution
- computational-biology
- deconvolution
PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"
Official implementation of JAMIE, Joint variational Autoencoders for Multimodal Imputation and Embedding
- autoencoder
- imputation
- integration
- multimodal
A flexible Julia toolkit for high-dimensional cellular profiles
- julia
- morphological-analysis
- high-content-screening