K-Dense-AI/scientific-agent-skills

这个仓库里有 166 个技能，GitHub 星标 ★ 45,217。

• adaptyvHow to use the Adaptyv Bio Foundry API and Python SDK for protein experiment des
• aeonThis skill should be used for time series machine learning tasks including class
• alphagenomeLook up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide v
• analytical-method-validationPlan, execute, and document validation, verification, and transfer of analytical
• anndataData structure for annotated matrices in single-cell analysis. Use when working
• arborAutonomously improve a real artifact (code, training recipe, agent harness, data
• arboretoInfer gene regulatory networks (GRNs) from gene expression data using scalable a
• astropyCore Python library for astronomy and astrophysics workflows that need Astropy A
• autoskillObserve the user's screen via screenpipe, detect repeated research workflows, ma
• benchling-integrationBenchling Python SDK and REST API integration for registry entities, inventory,
• bgpt-paper-searchSearch scientific papers and retrieve structured experimental data extracted fro
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• biopythonComprehensive molecular biology toolkit. Use for sequence manipulation, file par
• bioservicesUnified Python interface to 40+ bioinformatics services. Use when querying multi
• bulk-rnaseqEnd-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trim
• cellxgene-censusQuery the CZ CELLxGENE Census programmatically for versioned public single-cell
• cirqGoogle quantum computing framework. Use when targeting Google Quantum AI hardwar
• citation-managementComprehensive citation management for academic research. Search OpenAlex, PubMed
• clinical-decision-supportPrepare and validate research-only clinical decision-support evaluation, evidenc
• clinical-reportsCreate safety-bounded draft structures and run local deterministic checks for cl
• cobrapyConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux samp
• consciousness-councilRun a multi-perspective Mind Council deliberation on any question, decision, or
• daskDistributed computing for larger-than-RAM pandas/NumPy workflows. Use when you n
• database-lookupQuery documented public database APIs with explicit endpoints, filters, paginati
• dataladRetrieve, version, and publish scientific datasets with DataLad and git-annex, a
• datamolPythonic wrapper around RDKit with simplified interface and sensible defaults. P
• deepchemMolecular ML with diverse featurizers and pre-built datasets. Use for property p
• deepspot-mGenerate transcriptome-wide virtual spatial transcriptomics from H&E histology w
• deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprin
• depmapQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency sc
• dhdna-profilerExtract cognitive patterns and thinking fingerprints from any text. Use this ski
• diffdockDiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose p
• dnanexus-integrationBuild and operate reproducible genomics workloads on DNAnexus with the dx CLI, d
• docxUse this skill whenever the user wants to create, read, edit, or manipulate Word
• esmUse when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, For
• etetoolkitAnalyze, manipulate, compare, annotate, and visualize phylogenetic or other hier
• exa-searchWeb toolkit powered by Exa, tuned for scientific and technical content. Use this
• experimental-designDesign experiments and studies BEFORE data is collected — choosing a design, ran
• exploratory-data-analysisPerform bounded, local exploratory analysis of explicitly supported scientific f
• flowioRead, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files w
• fluidsimPlan, configure, inspect, restart, and analyze bounded FluidSim computational-fl
• folklore-variant-evidenceRetrieve ClinGen gene-disease validity assertions for a public gene or disease,
• generate-imageGenerate or edit images with AI models through the OpenRouter Image API (Gemini,
• genimlUse Geniml for audited local genomic-interval workflows: validate BED and univer
• genomic-coordinatesConvert genomic intervals between coordinate conventions, normalise and compare
• genomic-intelligencePredict regulatory features, gene structure, and expression directly from DNA se
• geomasterComprehensive geospatial science skill covering remote sensing, GIS, spatial ana
• geopandasGuidance and local audit tools for Python workflows that directly use GeoPandas
• get-available-resourcesDetect host inventory and effective CPU, memory, disk, scheduler, container, and
• ggetFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups:
• ginkgo-cloud-labSubmit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a w
• glycoengineeringAnalyze and engineer protein glycosylation. Scan sequences for N-glycosylation s
• gtarsUse Gtars for local genomic interval models and set algebra, overlaps and counts
• histolabLightweight WSI tile extraction and preprocessing. Use for basic slide processin
• hugging-scienceUse when the user is doing AI/ML work in a scientific domain such as biology, ch
• hypogenicPlans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothe
• hypothesis-generationFormulate evidence-bounded scientific questions, candidate hypotheses, rival exp
• imaging-data-commonsQuery and download public cancer imaging data from NCI Imaging Data Commons. Inv
• infographicsCreate professional infographics using Nano Banana Pro AI with smart iterative r
• iso-standards-readinessPrepares and structurally reviews readiness evidence for ISO management-system a
• lab-hardware-cadDesign custom laboratory hardware as parametric build123d models and export fabr
• labarchive-integrationSecurely integrate with the official LabArchives ELN REST-like API and Inventory
• lamindbUse when working with LaminDB, the open-source lineage-native lakehouse for biol
• latchbio-integrationBuild, register, debug, and operate bioinformatics workflows on Latch using the
• latex-postersCreate professional research posters in LaTeX using beamerposter, tikzposter, or
• liteparseLocal document and PDF parsing that returns spatial text with bounding boxes. Us
• literature-reviewConduct comprehensive, systematic literature reviews using multiple academic dat
• markdown-mermaid-writingComprehensive markdown and Mermaid diagram writing skill. Use when creating any
• market-research-reportsBuild evidence-traceable market research reports and assumption-driven market si
• markitdownConvert heterogeneous documents and selected URIs to Markdown with Microsoft Mar
• matchmsProcess, clean, compare, and search tandem mass spectra with matchms. Use for MS
• matlabBuild, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows
• matplotlibLow-level plotting library for full customization. Use when you need fine-graine
• medchemMedicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipi
• modalModal is a serverless cloud platform for running Python on demand, including on-
• molecular-dynamicsRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set u
• molfeatMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pre
• ncats-araxQueries the NCATS Translator ARAX production API for bounded, typed, provenance-
• networkxCreate, analyze, and visualize complex networks and graphs in Python with Networ
• neurokit2Use NeuroKit2 to build or audit reproducible research workflows for physiologica
• neuropixels-analysisAnalyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Cov
• nextflowBuild, run, and debug Nextflow data pipelines and nf-core workflows end to end.
• omero-integrationSecurely inspect and automate microscopy data workflows against OMERO.server wit
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• ontology-term-resolutionResolve free-text scientific labels to ontology term IDs and validate existing C
• open-notebookSelf-hosted, open-source alternative to Google NotebookLM for AI-powered researc
• openpivParticle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velo
• opentrons-integrationAuthor, review, migrate, simulate, and troubleshoot official Opentrons Python Pr
• optimize-for-gpuGPU-accelerates scientific Python on NVIDIA hardware and verifies that the resul
• pacsomaticOperator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM
• paper-lookupSearch 18 scholarly APIs for papers, preprints, citations, open-access full text
• paperclipSearch and read full-text biomedical papers, FDA/PMDA/EMA regulatory documents,
• paperzillaChat with your agent about projects, recommendations, and canonical papers in Pa
• parallel-webUse Parallel CLI for web search, URL extraction, deep research, structured data
• pathmlUse PathML for local, research-only computational pathology workflows: load and
• pathogen-variant-surveillanceQuery live pathogen genomic surveillance data through the GenSpectrum LAPIS API
• pathway-enrichmentRun pathway and gene-set enrichment analysis on gene lists or ranked gene data,
• pdfUse this skill whenever the user wants to do anything with PDF files. This inclu
• peer-reviewPrepare evidence-bounded, constructive peer-review drafts and structured manuscr
• pennylaneHardware-agnostic quantum ML framework with automatic differentiation. Use when
• phylogeneticsBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2
• pi-agentBuild with and use Pi, the minimal terminal coding harness. Use for installing P
• pkpd-modelingPharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental
• polarsHigh-performance DataFrame library for Python ETL, analytics, and pandas migrati
• polars-bioHigh-performance genomic interval operations and bioinformatics file I/O on Pola
• pptxUse this skill any time a .pptx or .potx file is involved in any way — as input,
• pptx-postersCreate and audit editable scientific posters in macro-free PowerPoint (.pptx) fr
• primekgQuery the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological
• protocolsio-integrationRead, validate, and safely export protocols.io data with current official REST/M
• pufferlibVersion-aware guidance for PufferLib reinforcement-learning environments, vector
• pydeseq2Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including
• pydicomUse pydicom to read, inspect, write, transform, and safely preflight local DICOM
• pyhealthBuild clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/si
• pylabrobotDevelop and review PyLabRobot lab-automation resources, liquid-handling plans, o
• pymatgenAnalyze, validate, convert, and transform materials structures and computed mate
• pymcBayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational
• pymooMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts
• pyopenmsComplete mass spectrometry analysis platform. Use for proteomics and metabolomic
• pysamPython/HTSlib workflows for genomic files. Use when reading, querying, filtering
• pytdcUse Therapeutics Data Commons through the PyTDC Python package for registry disc
• pytorch-lightningDeep learning framework (PyTorch Lightning / lightning package). Organize PyTorc
• pyzoteroInteract with Zotero reference management libraries using the pyzotero Python cl
• qiskitBuild, simulate, transpile, and execute quantum circuits with Qiskit and IBM Qua
• qutipSimulate and audit closed and open quantum-system models with QuTiP 5, including
• rdkitCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing,
• relsa-severity-assessmentMultivariate severity assessment and humane endpoint prediction for laboratory a
• research-grantsWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC.
• research-lookupCompile current scholarly evidence for a scientific manuscript or research brief
• rowanRowan is a cloud-native molecular modeling and medicinal-chemistry workflow plat
• scanpyStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimen
• scholar-evaluationProvide qualitative-first, evidence-traceable developmental review of scholarly
• scientific-brainstormingFacilitates evidence-aware scientific ideation with independent generation, stru
• scientific-critical-thinkingEvaluate scientific claims and evidence quality. Use for assessing experimental
• scientific-schematicsCreate publication-quality scientific diagrams using Nano Banana 2 AI with smart
• scientific-slidesBuild slide decks and presentations for research talks. Use this for making Powe
• scientific-visualizationCreate and audit truthful, accessible, publication-ready scientific figures with
• scientific-writingDraft, revise, and audit scientific manuscripts or reports with explicit evidenc
• scikit-bioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, dive
• scikit-learnMachine learning in Python with scikit-learn. Use when working with supervised l
• scikit-survivalBuild, evaluate, and audit right-censored or competing-risk survival workflows w
• scveloRNA velocity analysis with scVelo. Estimate cell state transitions from unsplice
• scvi-toolsDeep generative models for single-cell omics. Use when you need probabilistic ba
• seabornStatistical visualization with pandas integration. Use for quick exploration of
• shapExplain and audit machine-learning predictions with SHAP. Use for selecting SHAP
• simpyBuild, inspect, test, and analyze bounded process-based discrete-event simulatio
• stable-baselines3Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2
• statistical-analysisGuided statistical analysis for research data - test selection, assumption check
• statistical-powerSample-size and statistical power calculations for planning studies. Use wheneve
• statsmodelsStatistical models library for Python. Use when you need specific model classes
• sympyUse when you need exact symbolic math in Python — algebra, calculus, equation so
• tamarindAccess a collection of open-source molecular design and structural biology tools
• tiledbvcfEfficient storage and retrieval of genomic variant data using TileDB. Scalable V
• timesfm-forecastingZero-shot time series forecasting with Google's TimesFM foundation model. Use fo
• torch-geometricPyTorch Geometric (PyG) for graph neural networks — node/link/graph classificati
• torchdrugBuild and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property
• transformersHugging Face Transformers for loading Hub models, running pipeline inference, te
• treatment-plansFormat and structurally validate local treatment-plan documentation after clinic
• umap-learnUse UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, cluster
• uncertainty-and-unitsTrack physical units and propagate measurement uncertainty in scientific calcula
• usfiscaldataQuery the U.S. Treasury Fiscal Data REST API for federal financial data. No API
• vaexUse this skill for processing and analyzing large tabular datasets (billions of
• venue-templatesPrepare journal manuscripts, conference papers, research posters, and grant docu
• waypoint-bioUse when working with Outpost Bio's open microbiome foundation models - the Wayp
• what-if-oracleRun structured What-If scenario analysis with 4–6 branch possibility exploration
• xlsxCreate, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where
• zarr-pythonChunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, paralle