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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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3 of 5,674 resources
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)