Skills from K-Dense’s repositories that passed our trust, licence and security gates. Each keeps its author’s attribution.
| Repository | Tier | Verdict | Authorship | Checked | Skills |
|---|---|---|---|---|---|
| K-Dense-AI/claude-scientific-writer | Project | Approved · created 2025-10-27, pushed 2026-11-07, 2559 stars | Written in-house | 2026-11-07 | 26 |
| K-Dense-AI/scientific-agent-skills | Project | Approved · created 2025-10-19, pushed 2026-11-02, 56393 stars | Written in-house | 2026-11-07 | 177 |
Files are mirrored only where the licence allows redistribution; otherwise we link to the source.
K-Dense· Community
A structured framework for querying authoritative scientific and regulatory databases with reproducible provenance.
K-Dense· Community
Converts neuroscience imaging and behavioral data into validated Neurodata Without Borders (NWB) files.
K-Dense· Community
A lightweight Python library for reading, inspecting, and writing Flow Cytometry Standard (FCS) files.
K-Dense· Community
Develop and simulate Python protocols for Opentrons Flex and OT-2 liquid handling robots.
K-Dense· Community
Guides protocol selection, input preparation, and ordering for Ginkgo Bioworks Cloud Lab services.
K-Dense· Community
Process, clean, and compare tandem mass spectra for metabolomics and chemical analysis using matchms.
K-Dense· Community
A Python framework for managing annotated data matrices in single-cell genomics and general research workflows.
K-Dense· Community
A comprehensive framework for creating visually engaging, research-backed scientific presentations using AI-assisted design and structured workflows.
K-Dense· Community
Creates and customizes scientific plots with Matplotlib. Used for fine-grained control over plot elements, novel plot types, and scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.
K-Dense· Community
A structured, evidence-aware framework for facilitating scientific ideation, research prioritization, and transparent decision-making.
K-Dense· Community
A workflow for validating and executing RELION single-particle cryo-EM refinement and postprocessing.
K-Dense· Community
Simulate and audit closed and open quantum-system models using the QuTiP 5 framework.
K-Dense· Community
Comprehensive guidance for classical machine learning workflows using the scikit-learn Python library.
K-Dense· Community
Explain and audit machine-learning model predictions using the SHAP framework for feature attribution and visualization.
K-Dense· Community
Organize and review readiness evidence for ISO management-system and laboratory-competence standards.
K-Dense· Community
Local document and PDF parsing with spatial text extraction and bounding box support.
K-Dense· Community
Automates microscopy data workflows and metadata management for OMERO.server environments.
K-Dense· Community
A toolkit for performing web searches and batch URL content extraction using the Exa API, with specialized support for scholarly research.
K-Dense· Community
Build, test, and analyze process-based discrete-event simulations using the SimPy library.
K-Dense· Community
Queries a pinned Precision Medicine Knowledge Graph (PrimeKG) CSV for typed gene, drug, disease, and phenotype nodes, direct associations, disease context, and one- or two-hop paths. Use for PrimeKG reproducibility, biological association lookup, and hypothesis generation with relation and data provenance preserved.
K-Dense· Community
Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.
K-Dense· Community
A comprehensive tool for calculating statistical power and required sample sizes for research study planning.
K-Dense· Community
Integrates the Folklore Clinical Variant Interpretation MCP to retrieve public variant evidence, literature, and ClinGen gene-disease assertions.
K-Dense· Community
Build, simulate, and execute quantum circuits using Qiskit 2.x and IBM Quantum Runtime.