HIDE-Deconv

Scalable toolkit for analyzing single-cell gene expression data, including preprocessing, visualization, clustering, and trajectory inference.

OpenOncology is an open-source platform for precision oncology, designed to match tumor variants to approved therapies and perform de novo custom drug discovery when no existing option is available.

MCP server enabling spatial transcriptomics analysis via natural language, integrating 60+ methods including SpaGCN, Cell2location, LIANA+, CellRank for Visium, Xenium, MERFISH platforms

SQUARNA is a tool for RNA secondary structure prediction. It can take a single RNA sequence or an alignment of sequences as input. SQUARNA handles pseudoknots and can predict alternative structures. SQUARNA allows structural restraints and chemical probing data as additional input and is available at https://github.com/febos/SQUARNA and https://larnal.imol.institute/.

Open-source PyMOL plugin for membrane-aware review of predicted, designed and experimental protein structures. Membrane Visual QC provides planar membrane-relative geometry, residue core/interface classification, hydropathy and ligand-context review, solvent-accessibility context, PDBTM/OPM orientation-source checks, and reproducible batch reporting. It is designed as a review assistant rather than a biological structure validator.

Comprehensive collection of 125+ ready-to-use scientific skill modules for Claude AI across bioinformatics, cheminformatics, clinical research, ML, and materials science