Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
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Biological foundation modeling from molecular to genome scale
Cloud-native genomic dataframes and batch computing
- genetics
- vcf
- genomics
- gwas
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
- deep-learning
- protein-sequences
- protein-structure
- semi-supervised-learning
Spatial Single Cell Analysis in Python
- single-cell-rna-seq
- single-cell-genomics
- spatial-transcriptomics
- spatial-analysis
Graph-linked unified embedding for single-cell multi-omics data integration
- bioinformatics
- deep-learning
- single-cell
- single-cell-multiomics
Benchmarking analysis of data integration tools
UCE is a zero-shot foundation model for single-cell gene expression data
Schema and generated objects for biolink data model and upper ontology
- biolink
- monarchinitiative
- gene-ontology
- datamodel
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
- cellprofiler-analyst
- cellprofiler
- image-analysis
- machine-learning
OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.
Accurate and efficient spot detection for microscopy data
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).
- deep-generative-model
- deep-learning
- single-cell-data-integration
- single-cell-multiomics
Multigrate: multiomic data integration for single-cell genomics
Single-cell fluorescence microscopy data analysis
- microscopy
- fluorescence-microscopy-imaging
DeepAEG: A model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies