k-dense-ai
177 skills with substantive source documentation and an official publisher or observed installation demand. Read each skill’s original documentation through its card.
k-dense-aimarine-carbonate-chemistry
Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired total alkalinity, dissolved inorganic carbon, pH, or seawater pCO2/fCO2 measurements; carbonate speciation; aragonite and calcite saturation; Revelle factors; lab-to-in-situ temperature and pressure corrections; and measurement uncertainty propagation. Applies to carbonate-system calculations, not general aqueous speciation or air-sea gas-flux estimat
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimarkdown-mermaid-writing
Writes scientific Markdown documentation and Mermaid diagrams for workflows, relationships, timelines, and schemas. Provides syntax references, document templates, accessibility guidance, and version-aware rendering checks. Use when a user requests Markdown, Mermaid, or a text-based structural diagram; quantitative scientific figures require suitable plotting tools.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimarket-research-reports
Builds evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evidence, competitive landscapes, TAM/SAM/SOM reconciliation, forecast sensitivity, and auditable report scaffolds.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimarkitdown
Converts heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion. Covers safe local conversion, streams, Office/PDF/data formats, batch workflows, plugins, vision OCR, Azure extraction, and the official MCP server.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimatchms
Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks. Use pyopenms instead for LC-MS feature detection or proteomics pipelines.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimatlab
Builds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows. Use for arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimatplotlib
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.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimedchem
Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimodal
Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accelerated workloads (training, fine-tuning, inference), serving web endpoints, scheduling batch jobs, or scaling Python code to cloud containers with the Modal SDK.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimolecular-dynamics
Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aimolfeat
Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints, RDKit descriptors, pharmacophores, pretrained embeddings, configuration persistence, and molecule-to-label alignment.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aincats-arax
Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and inspection of TRAPI edge bindings, publications, and knowledge-source provenance. Do not use for inference, ranking, open-ended pathfinding, clinical guidance, or sensitive queries.
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-ainetworkx
Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks (random, scale-free, small-world), reading/writing graph file formats, or drawing network topologies. Common applications include social, biological, transportation, and citation networks.
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aineurokit2
Builds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, variability, and complexity. Use when code imports neurokit2 or needs its current APIs, schemas, and method-aware validation—not for diagnosis or device validation.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aineuropixels-analysis
Analyzes Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and unit curation (threshold-based, model-based UnitRefine, and AI-assisted visual review). Use when working with Neuropixels 1.0/2.0 recordings, spike sorting, or extracellular electrophysiology analysis.
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-ainextflow
Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. Use for Nextflow, nf-core, .nf files, nextflow.config, processes/channels/operators, samplesheets, nf-test, modules/subworkflows, container and executor configuration, HPC/SLURM or cloud deployment, and failed or resumed pipeline runs.
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-ainmrglue
Processes calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration regions. Use for raw 1D NMR processing, ppm-axis verification, apodization, Fourier transformation, manual phasing, baseline correction, or reproducible spectral integration.
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-ainwb-conversion
Converts neuroscience acquisition data to Neurodata Without Borders files with NeuroConv and PyNWB, preserves metadata and timebases, checks evidence-based clock alignment, and produces schema validation, NWB Inspector findings and round-trip checks. Use for NWB conversion and synchronization of planar single-channel two-photon TIFF imaging plus timestamped behavioral position CSV; this skill does not perform spike sorting or claim tested support for arbitrary acquisition formats.
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aiomero-integration
Inspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs. Use this skill for scoped OMERO inventory, metadata export, import/export planning, or reviewed write workflows.
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aionekgpd
Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individu
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aiontology-term-resolution
Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks up prefixes in Bioregistry, resolves compact identifiers via Identifiers.org, maps lab shorthand with ZOOMA, and builds Ontobee term pages. Use whenever an ontology identifier must be produced or checked - annotating tissue, cell type, disease, phenotype, assay, chemical, organism, sex, or developmental stage fields; preparing metadata for GEO, ENA, B
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- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aiopen-notebook
Organizes research with the self-hosted Open Notebook alternative to NotebookLM. Supports source ingestion (PDFs, web pages, audio, video, and Office documents), cited document chat, text and vector search, notes, custom transformations, and multi-speaker podcasts. Use when automating Open Notebook through its REST API or configuring its local or cloud AI providers, including OpenAI, Anthropic, Google, Ollama, Groq, and Mistral.
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aiopenpiv
Performs Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs, analyzing fluid dynamics or flow visualization experiments, cross-correlating interrogation windows, validating and replacing spurious PIV vectors, or computing vorticity, strain rate, and turbulence statistics from measured velocity fields.
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.
k-dense-aiopentrons-integration
Authors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for robot-specific liquid handling, deck and labware setup, pipettes, modules, runtime parameters, liquid classes, and Opentrons App analysis. Use pylabrobot instead when one workflow must support multiple robot vendors.
- Installationen
- 0
- GitHub Stars
- 54.615
- Aktualisiert
- 19. Okt.