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published by k-dense-ai
50 tools
- science-superpowersCore skills library: research framing, pre-registration, reproducible analysis, anomaly investigation, and review patterns372 stars
- denarioA set of ready to use scientific skills for Claude57,192 stars
- scientific-slides-k-dense-ai-claude-scientific-sBuild slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, rese57,192 stars
- flowio-k-dense-ai-claude-scientific-sParse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for fl57,192 stars
- cirq-k-dense-ai-claude-scientific-sGoogle quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum charac57,192 stars
- histolabA set of ready to use scientific skills for Claude57,192 stars
- pdfA set of ready to use scientific skills for Claude57,192 stars
- paper-2-web-k-dense-ai-claude-scientific-sThis skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2We57,192 stars
- 13c-metabolic-fluxEstimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope s57,192 stars
- adaptyvUses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor la57,192 stars
- aeonThis skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly dete57,192 stars
- analytical-method-validationPlans, executes, and documents validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) an57,192 stars
- anndataHandles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data forma57,192 stars
- arboretoInfers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for tra57,192 stars
- astropyCore Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tabl57,192 stars
- autoskillAnalyzes user-requested Screenpipe history windows to detect repeated research workflows, match existing scientific skills, and stage new sk57,192 stars
- benchling-integrationBenchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse q57,192 stars
- bgpt-paper-searchSearches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported57,192 stars
- biopythonProvides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access57,192 stars
- bioservicesProvides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-datab57,192 stars
- cellprofilerRuns reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Support57,192 stars
- cellxgene-censusQueries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need popula57,192 stars
- cirqGoogle quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum charac57,192 stars
- citation-managementComprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, 57,192 stars
- clinical-decision-supportPrepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and57,192 stars
- clinical-reportsCreates safety-bounded draft structures and runs local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate rese57,192 stars
- cobrapyPerforms constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production57,192 stars
- consciousness-councilStructures a multi-perspective council exercise for decisions, research trade-offs, and creative challenges. Simulates thinking archetypes, 57,192 stars
- daskScales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask. Covers DataFrames, Arrays, Bags, Futu57,192 stars
- database-lookupQueries documented public database APIs with explicit endpoints, filters, pagination, and provenance. Used when a scientific, regulatory, fi57,192 stars
- datamolPythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsin57,192 stars
- deepchemBuilds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, 57,192 stars
- deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, 57,192 stars
- depmapRetrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics b57,192 stars
- dhdna-profilerApplies the DHDNA framework as an exploratory rubric for reasoning and writing patterns in supplied text. Used for explicit requests for DHD57,192 stars
- diffdockPredicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, 57,192 stars
- dnanexus-integrationBuilds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextf57,192 stars
- docxCreates, reads, edits, and manipulates Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word 57,192 stars
- esmUses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference57,192 stars
- etetoolkitAnalyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I57,192 stars
- exa-searchSearches scientific and technical web content with Exa and extracts page or PDF text from URLs in batches. Supports scholarly discovery with57,192 stars
- exploratory-data-analysisPerforms bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional Num57,192 stars
- flowioReads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel in57,192 stars
- fluidsimPlans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validi57,192 stars
- folklore-variant-evidenceRetrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature fo57,192 stars
- generate-imageGenerates or edits images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos,57,192 stars
- genimlSupports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect mode57,192 stars
- geomasterSupports geospatial research workflows for remote sensing, vector and raster GIS, spatial statistics, terrain and network analysis, and mach57,192 stars
- geopandasGuidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data 57,192 stars
- get-available-resourcesDetects host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware pla57,192 stars
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