k-dense-ai/scientific-agent-skills
59 skills · 45,413 total installs
$npx skills add k-dense-ai/scientific-agent-skillsSkillInstalls
citation-managementComprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and…exploratory-data-analysisPerform bounded, local exploratory analysis of explicitly supported scientific files.docxUse this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files).database-lookupQuery documented public database APIs with explicit endpoints, filters, pagination, and provenance.hypothesis-generationFormulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions,…bgpt-paper-searchSearch scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.generate-imageGenerate or edit images with AI models through the OpenRouter Image API (Gemini, FLUX, Seedream, Recraft, GPT-Image).aeonThis skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection,…get-available-resourcesDetect host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a…infographicsCreate professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review.daskDistributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters.hypogenicPlans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text datasets.biopythonComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access…consciousness-councilRun a multi-perspective Mind Council deliberation on any question, decision, or creative challenge.geopandasGuidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.clinical-reportsCreate safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports.bioservicesUnified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with…anndataData structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem.geomasterComprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains.ggetFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures,…clinical-decision-supportPrepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance…deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq…benchling-integrationBenchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries.adaptyvHow to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval.deepchemMolecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive…datamolPythonic wrapper around RDKit with simplified interface and sensible defaults.imaging-data-commonsQuery and download public cancer imaging data from NCI Imaging Data Commons using idc-index.fluidsimPlan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety…astropyCore Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems,…cellxgene-censusQuery the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data.arboretoInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).esmUse when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.dhdna-profilerExtract cognitive patterns and thinking fingerprints from any text.depmapQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles.genimlUse Geniml for audited local genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer…diffdockDiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual…flowioRead, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO.cirqGoogle quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization…labarchive-integrationSecurely integrate with the official LabArchives ELN REST-like API and Inventory API v1.gtarsUse Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase…etetoolkitAnalyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4.histolabLightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images.cobrapyConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.dnanexus-integrationBuild and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow.lamindbUse when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models.latchbio-integrationBuild, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic…glycoengineeringAnalyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated…ginkgo-cloud-labSubmit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation…hugging-scienceUse when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology,…autoskillObserve the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or…exa-searchWeb toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content.bidsUse this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET,…bulk-rnaseqEnd-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon,…experimental-designDesign experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are…arborAutonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree…genomic-intelligencePredict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no…genomic-coordinatesConvert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before…analytical-method-validationiso-standards-readiness