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
Stores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results, allele statistics, QC, and VCF/BCF export locally or through TileDB Cloud.
K-Dense· Community
Accelerate scientific Python workloads on NVIDIA GPUs using the RAPIDS ecosystem and custom kernels.
K-Dense· Community
Guidance and local audit tools for Python workflows using GeoPandas 1.2.0 for spatial data analysis.
K-Dense· Community
Perform genomic interval arithmetic and bioinformatics file I/O using Polars DataFrames.
K-Dense· Community
Query, filter, and download public cancer imaging datasets from the NCI Imaging Data Commons.
K-Dense· Community
Develop and simulate lab automation protocols using the PyLabRobot 0.2.2 framework.
K-Dense· Community
A Python toolkit for analyzing, manipulating, and visualizing phylogenetic and hierarchical trees using ETE 4.
K-Dense· Community
A comprehensive toolkit for pharmacokinetic and pharmacodynamic modeling, simulation, and data analysis.
K-Dense· Community
A comprehensive Python library for computational molecular biology, sequence analysis, and bioinformatics workflows.
K-Dense· Community
A lightweight utility for converting diverse document formats into structured Markdown for analysis, search, and LLM ingestion.
K-Dense· Community
Automated QIIME 2 workflow for processing paired-end 16S amplicon sequencing data with provenance tracking.
K-Dense· Community
Resolves and validates scientific labels against standard ontologies using EBI OLS4, Bioregistry, and other research-focused identifier services.
K-Dense· Community
A toolkit for working with Outpost Bio's Waypoint microbiome foundation models and the Compass benchmark.
K-Dense· Community
Perform exact symbolic mathematics, calculus, and equation solving using the SymPy Python library.
K-Dense· Community
Query and analyze public pathogen genomic surveillance data from GenSpectrum and Pathoplexus LAPIS deployments.
K-Dense· Community
Perform bulk RNA-seq differential expression analysis using PyDESeq2 with support for GLMs, Wald tests, and LFC shrinkage.
K-Dense· Community
Compiles verified scholarly evidence and creates a structured research packet for scientific manuscripts.
K-Dense· Community
Build, run, and debug reproducible data pipelines using Nextflow DSL2 and nf-core workflows.
K-Dense· Community
Automated equilibrium phase calculations for thermodynamic TDB databases using pycalphad.
K-Dense· Community
A research-only toolkit for documenting and validating clinical decision-support evaluation, governance, and evidence-profile artifacts.
K-Dense· Community
Integrate with Benchling using the Python SDK and REST API to automate lab data, registry entities, inventory, and ELN workflows.
K-Dense· Community
Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.7 Flash for quality review. Refines when the review requests improvement, with at most two generations. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
K-Dense· Community
A comprehensive toolkit for fitting, diagnosing, and interpreting statistical models including regression, GLMs, and time series analysis in Python.
K-Dense· Community
Build, differentiate, and optimize quantum circuits and hybrid quantum-classical models using PennyLane.