Entry
Appears in 4 awesome lists
[Python] An MCP server enabling spatial transcriptomics analysis via natural language. Integrates 60+ methods including SpaGCN, Cell2location, RCTD, LIANA+, CellRank for spatial domains, deconvolution, cell communication, and trajectory analysis. Supports Visium, Xenium, MERFISH, Slide-seq.…
Section: Biology & Medicine · MCP server enabling spatial transcriptomics analysis via natural language, integrating 60+ methods including SpaGCN, Cell2location, LIANA+, CellRank for Visium, Xenium, MERFISH platforms
Section: Preprocessing Tools · MCP server for spatial transcriptomics analysis via natural language.
Section: Spatial transcriptomics · [Python] An MCP server enabling spatial transcriptomics analysis via natural language. Integrates 60+ methods including SpaGCN, Cell2location, RCTD, LIANA+, CellRank for spatial domains, deconvolution, cell communication, and trajectory analysis. Supports Visium, Xenium, MERFISH, Slide-seq.…
Section: Tools · MCP server enabling spatial transcriptomics analysis via natural language. Integrates 60+ methods for spatial domains, deconvolution, cell communication, and trajectory analysis.
Interactive personal genome analysis toolkit using Claude Code and Python. Parses raw genotyping data from consumer DNA services and analyzes SNPs across 17 categories including health risks, pharmacogenomics, ancestry, and nutrition, with a terminal-style HTML dashboard.
Democratizing deep learning for drug discovery, quantum chemistry, materials science, and biology. High-quality open-source toolchain with 50+ models and extensive tutorials. MIT licensed.
Image viewer and image processing tool. Fiji - General purpose tool. Image viewer and image processing tool. vizarr - Browser-based image viewer for zarr format. avivator - Browser-based image viewer for tiff files. OMERO - Image viewer for high-content screening. IDR uses OMERO. Intro fiftyone -…
Cheminformatics software & machine learning toolkit.
Machine learning and statistical learning for neuroimaging in Python, providing easy-to-use tools for fMRI and MRI analysis including decoding, connectivity estimation, and parcellation with seamless scikit-learn integration (INRIA Parietal team, 1.4K+ stars)
Open-source biomolecular interaction prediction models. Boltz-1 was the first fully open source model to approach AlphaFold3 accuracy; Boltz-2 adds binding affinity prediction for drug discovery. MIT licensed.
Local-first, open-source healthcare AI toolkit for clinical NLP and PHI/PII de-identification across 12 languages, running entirely on-device with 1,000+ specialized medical models; provides Python SDK, REST API, Docker deployment, and native Swift apps via OpenMedKit with Apple MLX/CoreML…
Multi-LLM consensus framework for automated cell type annotation in single-cell transcriptomics, integrating predictions from 10+ large language models with iterative discussion and uncertainty quantification to reduce single-model biases, achieving up to 95% accuracy without reference datasets;…