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
Repository Index
47,133 repositories indexed
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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 repository host gives no description.
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
The repository host gives no description.
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
The repository host gives no description.
Multigrate: multiomic data integration for single-cell genomics
CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
- cancer
- foundation-model
- single-cell
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"
Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.
- postgres
- postgresql
- python
- infectious-disease
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
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.
XitoSBML - the spatial SBML plugin for ImageJ
- sbml
- systems-biology
- spatial-sbml-plugin
- imagej
Interpretable modeling of cellular responses to drug perturbations using cycle consistence learning