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Cross-domain directory aggregating tools, AI models, datasets, and research resources from bio.tools, Bioconductor, HuggingFace, curated GitHub awesome-lists, and more.
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4 of 5,684 resources
Machine learning model predicting cellular perturbation response across diverse contexts with State Transition (ST) and State Embedding (SE) variants, featuring CLI tooling, PyPI distribution, and Virtual Cell Challenge integration (575+ stars)
Unified Python framework for bulk, single-cell, and spatial RNA-seq multi-omics analysis with deep learning deconvolution (VAE) and graph neural networks, bridging Bindea, Bindea, scanpy and squidpy ecosystems (Nature Communications 2024)
Transformer encoder-decoder for de novo peptide sequencing from tandem mass spectrometry, translating MS/MS spectra directly to peptide sequences without reference databases, enabling identification of novel peptides for immunopeptidomics, antibody repertoires, and metaproteomes (Noble Lab UW, Nature Communications 2024)
Unified framework for state-of-the-art pre-trained bio foundation models across genomics and transcriptomics, providing standardized interfaces and pipelines for DNA, RNA, and single-cell models including Evo 2, Geneformer, scGPT, and UCE with streamlined inference, benchmarking, and fine-tuning workflows (213+ stars, 2024-2025)