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168 skills listed · Best: Literature review

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SkillNo. 01Conduct comprehensive, systematic literature reviewsLiterature review

K-Dense-AI/scientific-agent-skills · by K-Dense-AIConduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when c…★ 46k GitHub starsFree

SkillNo. 02Comprehensive molecular biology toolkitBiopython: Computational Molecular Biology in Python

K-Dense-AI/scientific-agent-skills · by K-Dense-AIComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez)…★ 46k GitHub starsFree

SkillNo. 03Fast CLI/Python queries to 20+ bioinformatics databasesGget

K-Dense-AI/scientific-agent-skills · by K-Dense-AIFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysi…★ 46k GitHub starsFree

SkillConduct comprehensive, systematic literature reviewsLiterature review

K-Dense-AI/scientific-agent-skills · by K-Dense-AIConduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when c…★ 46k GitHub starsFree

SkillComprehensive molecular biology toolkitBiopython: Computational Molecular Biology in Python

K-Dense-AI/scientific-agent-skills · by K-Dense-AIComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez)…★ 46k GitHub starsFree

SkillFast CLI/Python queries to 20+ bioinformatics databasesGget

K-Dense-AI/scientific-agent-skills · by K-Dense-AIFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysi…★ 46k GitHub starsFree

SkillPrepare evidence-boundedPeer review

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPrepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized review of scientific manuscripts, protocols, preprint…★ 46k GitHub starsFree

SkillDraft, revise, and audit scientific manuscripts or reportsScientific writing

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDraft, revise, and audit scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality co…★ 46k GitHub starsFree

SkillUnified Python interface to 40+ bioinformatics servicesBioservices

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUnified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API.…★ 46k GitHub starsFree

SkillComprehensive citation management for academic research

K-Dense-AI/scientific-agent-skills · by K-Dense-AIComprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and gener…★ 46k GitHub starsFree

SkillFormulate evidence-bounded scientific questionsScientific Hypothesis Generation

K-Dense-AI/scientific-agent-skills · by K-Dense-AIFormulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and…★ 46k GitHub starsFree

SkillBuild slide decks and presentations for research talksScientific slides

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis de…★ 46k GitHub starsFree

SkillStandard single-cell RNA-seq analysis pipelineScanpy: Single-Cell Analysis

K-Dense-AI/scientific-agent-skills · by K-Dense-AIStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization,…★ 46k GitHub starsFree

SkillBenchling Python SDK and REST API integration for registryBenchling integration

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBenchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating l…★ 46k GitHub starsFree

SkillMolecular ML with diverse featurizers and pre-built datasetsDeepchem

K-Dense-AI/scientific-agent-skills · by K-Dense-AIMolecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featuriza…★ 46k GitHub starsFree

SkillDifferential gene expression analysis for bulk RNA-seqPydeseq2

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDifferential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.★ 46k GitHub starsFree

SkillAnalyze, validate, convertPymatgen

K-Dense-AI/scientific-agent-skills · by K-Dense-AIAnalyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs, including local phase diagrams, symmetry sensitivi…★ 46k GitHub starsFree

SkillBayesian modeling with PyMCPyMC Bayesian Modeling

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and infe…★ 46k GitHub starsFree

SkillPyTorch Geometric for graph neuralPyTorch Geometric (PyG)

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling,…★ 46k GitHub starsFree

SkillEvaluate scientific claims and evidence qualityScientific critical thinking

K-Dense-AI/scientific-agent-skills · by K-Dense-AIEvaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks…★ 46k GitHub starsFree

SkillCreate publication-quality scientific diagrams using NanoScientific Schematics and Diagrams

K-Dense-AI/scientific-agent-skills · by K-Dense-AICreate publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Only regenerates if qual…★ 46k GitHub starsFree

SkillData structure for annotated matrices in single-cellAnndata

K-Dense-AI/scientific-agent-skills · by K-Dense-AIData structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill…★ 46k GitHub starsFree

SkillQuery the CZ CELLxGENE Census programmatically for versioned

K-Dense-AI/scientific-agent-skills · by K-Dense-AIQuery the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene…★ 46k GitHub starsFree

SkillPythonic wrapper around RDKit with simplified interfaceDatamol Cheminformatics Skill

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descripto…★ 46k GitHub starsFree

SkillNGS analysis toolkitdeepTools: NGS Data Analysis Toolkit

K-Dense-AI/scientific-agent-skills · by K-Dense-AINGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.★ 46k GitHub starsFree

SkillBuild and operate reproducible genomics workloadsDnanexus integration

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus data tran…★ 46k GitHub starsFree

SkillPerform bounded, local exploratory analysis of explicitlyExploratory data analysis

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPerform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basi…★ 46k GitHub starsFree

SkillCreate professional research posters in LaTeXLaTeX Research Posters

K-Dense-AI/scientific-agent-skills · by K-Dense-AICreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communi…★ 46k GitHub starsFree

SkillConvert heterogeneous documents and selected URIsMarkitdown

K-Dense-AI/scientific-agent-skills · by K-Dense-AIConvert heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion. Covers safe local conversion, s…★ 46k GitHub starsFree

SkillMulti-objective optimization frameworkPymoo - Multi-Objective Optimization in Python

K-Dense-AI/scientific-agent-skills · by K-Dense-AIMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization pr…★ 46k GitHub starsFree

SkillDeep learning frameworkPytorch lightning

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDeep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipeli…★ 46k GitHub starsFree

SkillCheminformatics toolkit for fine-grained molecular controlRDKit Cheminformatics Toolkit

K-Dense-AI/scientific-agent-skills · by K-Dense-AICheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, simila…★ 46k GitHub starsFree

SkillCreate and audit truthful, accessibleScientific visualization

K-Dense-AI/scientific-agent-skills · by K-Dense-AICreate and audit truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use for figure design, multi-panel layouts, uncertainty…★ 46k GitHub starsFree

SkillMachine learning in Python with scikit-learn

K-Dense-AI/scientific-agent-skills · by K-Dense-AIMachine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality r…★ 46k GitHub starsFree

SkillTest selection, assumption checking, effect sizesStatistical analysis

K-Dense-AI/scientific-agent-skills · by K-Dense-AIGuided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting. Us…★ 46k GitHub starsFree

SkillUse UMAP-learn for nonlinear dimensionality reduction

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP, and Parametr…★ 46k GitHub starsFree

SkillChunked N-D arrays for cloud storageZarr python

K-Dense-AI/scientific-agent-skills · by K-Dense-AIChunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec, NumPy/Dask/Xarray compatible, for large-scale scientific comput…★ 46k GitHub starsFree

SkillCore Python library for astronomy and astrophysics workflowsAstropy

K-Dense-AI/scientific-agent-skills · by K-Dense-AICore Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and co…★ 46k GitHub starsFree

SkillConstraint-based metabolic modelingCOBRApy - Constraint-Based Reconstruction and Analysis

K-Dense-AI/scientific-agent-skills · by K-Dense-AIConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.★ 46k GitHub starsFree

SkillCreating any scientific document, report, analysisMarkdown and Mermaid Writing

K-Dense-AI/scientific-agent-skills · by K-Dense-AIComprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams…★ 46k GitHub starsFree

SkillMedicinal chemistry filters for compound triageMedchem

K-Dense-AI/scientific-agent-skills · by K-Dense-AIMedicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, a…★ 46k GitHub starsFree

SkillMolecular featurization for MLMolfeat - Molecular Featurization Hub

K-Dense-AI/scientific-agent-skills · by K-Dense-AIMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.★ 46k GitHub starsFree

SkillComplete mass spectrometry analysis platformPyopenms

K-Dense-AI/scientific-agent-skills · by K-Dense-AIComplete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free and isobaric qu…★ 46k GitHub starsFree

SkillCompile current scholarly evidenceResearch lookup

K-Dense-AI/scientific-agent-skills · by K-Dense-AICompile current scholarly evidence for a scientific manuscript or research brief. Use when the user explicitly asks to gather literature, references, background evidence…★ 46k GitHub starsFree

SkillBiological data toolkitScikit bio

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for…★ 46k GitHub starsFree

SkillHugging Face Transformers for loading Hub models

K-Dense-AI/scientific-agent-skills · by K-Dense-AIHugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimodal tasks. Use w…★ 46k GitHub starsFree

SkillInfer gene regulatory networks from gene expression dataArboreto

K-Dense-AI/scientific-agent-skills · by K-Dense-AIInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, sin…★ 46k GitHub starsFree

SkillPrepare and validate research-only clinical decision-supportClinical Decision-Support Research and Evaluation

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPrepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Use for…★ 46k GitHub starsFree

SkillDiffDock and DiffDock-L molecular dockingDiffDock: Molecular Docking with Diffusion Models

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, an…★ 46k GitHub starsFree

SkillAnalyze, manipulate, compare, annotateETE Toolkit 4

K-Dense-AI/scientific-agent-skills · by K-Dense-AIAnalyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matc…★ 46k GitHub starsFree

SkillRead, inspect, and write Flow Cytometry Standard 2.0, 3.0Flowio

K-Dense-AI/scientific-agent-skills · by K-Dense-AIRead, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, NumPy event extraction…★ 46k GitHub starsFree

SkillQuery and download public cancer imaging data from NCIImaging data commons

K-Dense-AI/scientific-agent-skills · by K-Dense-AIQuery and download public cancer imaging data from NCI Imaging Data Commons. Invoke for any question about IDC collections, cancer imaging datasets, DICOM data access, r…★ 46k GitHub starsFree

SkillSecurely inspect and automate microscopy data workflowsOmero integration

K-Dense-AI/scientific-agent-skills · by K-Dense-AISecurely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented…★ 46k GitHub starsFree

SkillHigh-performance DataFrame library for Python ETL, analyticsPolars

K-Dense-AI/scientific-agent-skills · by K-Dense-AIHigh-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization, parallel exe…★ 46k GitHub starsFree

SkillCreate and audit editable scientific posters in macro-freePptx posters

K-Dense-AI/scientific-agent-skills · by K-Dense-AICreate and audit editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets. Use when the requested deliverable is a Powe…★ 46k GitHub starsFree

SkillUse Therapeutics Data Commons through the PyTDC PythonPyTDC (Therapeutics Data Commons)

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset access, task-aware splits, evaluator metrics, benchmark groups, a…★ 46k GitHub starsFree

SkillProvide qualitative-firstScholar evaluation

K-Dense-AI/scientific-agent-skills · by K-Dense-AIProvide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quality contro…★ 46k GitHub starsFree

SkillFacilitates evidence-aware scientific ideationScientific brainstorming

K-Dense-AI/scientific-agent-skills · by K-Dense-AIFacilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and…★ 46k GitHub starsFree

SkillStatistical visualization with pandas integrationSeaborn Statistical Visualization

K-Dense-AI/scientific-agent-skills · by K-Dense-AIStatistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best…★ 46k GitHub starsFree

SkillEfficient storage and retrieval of genomic variant dataTiledbvcf

K-Dense-AI/scientific-agent-skills · by K-Dense-AIEfficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and…★ 46k GitHub starsFree

SkillBuild, register, debug, and operate bioinformatics workflowsLatchbio integration

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, an…★ 46k GitHub starsFree

SkillLow-level plotting library for full customizationMatplotlib

K-Dense-AI/scientific-agent-skills · by K-Dense-AILow-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specifi…★ 46k GitHub starsFree

SkillAnalyze Neuropixels extracellular recordings end-to-endNeuropixels Data Analysis

K-Dense-AI/scientific-agent-skills · by K-Dense-AIAnalyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosor…★ 46k GitHub starsFree

SkillPython/HTSlib workflows for genomic filesPysam

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPython/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pile…★ 46k GitHub starsFree

SkillWrite competitive research proposals for NSF, NIH, DOEResearch Grant Writing

K-Dense-AI/scientific-agent-skills · by K-Dense-AIWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, signifi…★ 46k GitHub starsFree

SkillStatistical models library for PythonStatsmodels: Statistical Modeling and Econometrics

K-Dense-AI/scientific-agent-skills · by K-Dense-AIStatistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best…★ 46k GitHub starsFree

SkillDistributed computing for larger-than-RAM pandas/NumPyDask

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDistributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parall…★ 46k GitHub starsFree

SkillProcess, clean, compare, and search tandem mass spectraMatchms

K-Dense-AI/scientific-agent-skills · by K-Dense-AIProcess, clean, compare, and search tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matchi…★ 46k GitHub starsFree

SkillModal is a serverless cloud platform for running Python

K-Dense-AI/scientific-agent-skills · by K-Dense-AIModal 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 workload…★ 46k GitHub starsFree

SkillFormat and structurally validate local treatment-planTreatment-Plan Documentation

K-Dense-AI/scientific-agent-skills · by K-Dense-AIFormat and structurally validate local treatment-plan documentation after clinical decisions have already been supplied and verified by authorized licensed professionals…★ 46k GitHub starsFree

SkillCreate safety-bounded draft structures and run localClinical reports

K-Dense-AI/scientific-agent-skills · by K-Dense-AICreate safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with syn…★ 46k GitHub starsFree

SkillUse Gtars for local genomic interval models and set algebra

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning…★ 46k GitHub starsFree

SkillLightweight WSI tile extraction and preprocessingHistolab

K-Dense-AI/scientific-agent-skills · by K-Dense-AILightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images. Best for si…★ 46k GitHub starsFree

SkillPlans and audits use of ChicagoHAI HypoGeniC/HypoRefine

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPlans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text datasets. Use for the `hypogenic` package, its task conf…★ 46k GitHub starsFree

SkillSecurely integrate with the official LabArchives ELNLabArchives Integration

K-Dense-AI/scientific-agent-skills · by K-Dense-AISecurely integrate with the official LabArchives ELN REST-like API and Inventory API v1. Use for regional endpoint selection, signed-request construction, user authoriza…★ 46k GitHub starsFree

SkillAuthor, review, migrate, simulateOpentrons integration

K-Dense-AI/scientific-agent-skills · by K-Dense-AIAuthor, review, migrate, simulate, and troubleshoot official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for robot-specific liquid handling,…★ 46k GitHub starsFree

SkillDevelop and review PyLabRobot lab-automation resources

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDevelop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Use for PyLabRobot protocols or AP…★ 46k GitHub starsFree

SkillProduction-ready reinforcement learning algorithmsStable baselines3

K-Dense-AI/scientific-agent-skills · by K-Dense-AIProduction-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and we…★ 46k GitHub starsFree

SkillZero-shot time series forecasting with Google's TimesFMTimesfm forecasting

K-Dense-AI/scientific-agent-skills · by K-Dense-AIZero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a…★ 46k GitHub starsFree

SkillBuild and troubleshoot TorchDrug 0.2.1 workflows

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein rep…★ 46k GitHub starsFree

SkillPrepare journal manuscripts, conference papersVenue templates

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPrepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting guidance and bundled LaTeX scaffolds. Use when sele…★ 46k GitHub starsFree

SkillAeon Time Series Machine Learning

K-Dense-AI/scientific-agent-skills · by K-Dense-AIThis skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and simi…★ 46k GitHub starsFree

SkillWorking directly with the esm Python SDKESM: Evolutionary Scale Modeling

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.★ 46k GitHub starsFree

SkillCreate professional infographics using Nano Banana Pro AI

K-Dense-AI/scientific-agent-skills · by K-Dense-AICreate professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Integrates research-lookup and web s…★ 46k GitHub starsFree

SkillCreate, analyze, and visualize complex networksNetworkx

K-Dense-AI/scientific-agent-skills · by K-Dense-AICreate, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph algorithms (shor…★ 46k GitHub starsFree

SkillUse PathML for local, research-only computational pathology

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and QC pipelines, manage h5path data, quantify multiplex…★ 46k GitHub starsFree

SkillVersion-aware guidance for PufferLib reinforcement-learning

K-Dense-AI/scientific-agent-skills · by K-Dense-AIVersion-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review. Use when ada…★ 46k GitHub starsFree

SkillBuild clinical/healthcare deep-learning pipelines withPyhealth

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), definin…★ 46k GitHub starsFree

SkillDeep generative models for single-cell omicsScvi tools

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDeep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or mu…★ 46k GitHub starsFree

SkillBuild, inspect, test, and analyze bounded process-basedSimpy

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild, inspect, test, and analyze bounded process-based discrete-event simulations with SimPy, including events, resources, interrupts, monitoring, replications, warm-up…★ 46k GitHub starsFree

SkillGoogle quantum computing frameworkCirq - Quantum Computing with Python

K-Dense-AI/scientific-agent-skills · by K-Dense-AIGoogle quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best…★ 46k GitHub starsFree

SkillPlan, configure, inspect, restartFluidsim

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPlan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks. Use for…★ 46k GitHub starsFree

SkillDetect host inventory and effective CPU, memory, diskGet available resources

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDetect host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a clearly reso…★ 46k GitHub starsFree

SkillWorking with LaminDB, the open-source lineage-native

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, lineage tr…★ 46k GitHub starsFree

SkillBuild evidence-traceable market research reports

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evidence, co…★ 46k GitHub starsFree

SkillUse NeuroKit2 to build or audit reproducible research

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse NeuroKit2 to build or audit reproducible research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, variability,…★ 46k GitHub starsFree

SkillYou need exact symbolic math inSymPy - Symbolic Mathematics in Python

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code generation via lambdify/LaTeX. Prefer NumPy or Sc…★ 46k GitHub starsFree

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy ev…★ 46k GitHub starsFree

SkillHow to use the Adaptyv Bio Foundry API and Python SDK

K-Dense-AI/scientific-agent-skills · by K-Dense-AIHow to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv…★ 46k GitHub starsFree

SkillQuery documented public database APIs with explicitDatabase lookup

K-Dense-AI/scientific-agent-skills · by K-Dense-AIQuery documented public database APIs with explicit endpoints, filters, pagination, and provenance. Use when a scientific, regulatory, financial, or other database-backe…★ 46k GitHub starsFree

SkillUse Parallel CLI for web search, URL extractionParallel Web Toolkit

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and recurring web monitoring. Best for requests that explic…★ 46k GitHub starsFree

SkillHardware-agnostic quantum ML framework with automaticPennylane

K-Dense-AI/scientific-agent-skills · by K-Dense-AIHardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or nee…★ 46k GitHub starsFree

SkillRead, validate, and safely export protocols.io dataprotocols.io Integration

K-Dense-AI/scientific-agent-skills · by K-Dense-AIRead, validate, and safely export protocols.io data with current official REST/MCP contracts, or create non-executing mutation plans. The bundled client makes bounded of…★ 46k GitHub starsFree

SkillUse pydicom to read, inspect, write, transform

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse pydicom to read, inspect, write, transform, and safely preflight local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression plugi…★ 46k GitHub starsFree

SkillBuild, simulate, transpileQiskit

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitiv…★ 46k GitHub starsFree

SkillBuild, evaluate, and audit right-censored or competing-riskScikit survival

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild, evaluate, and audit right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model selection, probability p…★ 46k GitHub starsFree

SkillExplain and audit machine-learning predictions with SHAP

K-Dense-AI/scientific-agent-skills · by K-Dense-AIExplain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and validating feature attributions, handling multi-ou…★ 46k GitHub starsFree

SkillGuidance and local audit tools for Python workflowsGeopandas

K-Dense-AI/scientific-agent-skills · by K-Dense-AIGuidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.★ 46k GitHub starsFree

SkillSimulate and audit closed and open quantum-system modelsQuTiP 5

K-Dense-AI/scientific-agent-skills · by K-Dense-AISimulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. Use for lo…★ 46k GitHub starsFree

SkillObserve the user's screen via screenpipeAutoskill

K-Dense-AI/scientific-agent-skills · by K-Dense-AIObserve the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition r…★ 46k GitHub starsFree

SkillSelf-hosted, open-source alternative to Google NotebookLMOpen notebook

K-Dense-AI/scientific-agent-skills · by K-Dense-AISelf-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting…★ 46k GitHub starsFree

SkillWeb toolkit powered by ExaExa Web Toolkit

K-Dense-AI/scientific-agent-skills · by K-Dense-AIWeb 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. Covers: web se…★ 46k GitHub starsFree

SkillComprehensive geospatial science skill covering remoteGeomaster

K-Dense-AI/scientific-agent-skills · by K-Dense-AIComprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satel…★ 46k GitHub starsFree

SkillGPU-accelerates scientific Python on NVIDIA hardwareGPU Optimization for Python with NVIDIA

K-Dense-AI/scientific-agent-skills · by K-Dense-AIGPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster. Use for CUDA/GPU optimization; CPU-bound NumPy, SciPy, pandas, s…★ 46k GitHub starsFree

SkillHugs scienceHugging science

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, eng…★ 46k GitHub starsFree

SkillSearch 18 scholarly APIs for papers, preprints, citationsPaper lookup

K-Dense-AI/scientific-agent-skills · by K-Dense-AISearch 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA status, and return results with reproducible provena…★ 46k GitHub starsFree

SkillInteract with Zotero reference management librariesPyzotero

K-Dense-AI/scientific-agent-skills · by K-Dense-AIInteract with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via…★ 46k GitHub starsFree

SkillQuery the U.SU.S. Treasury Fiscal Data API

K-Dense-AI/scientific-agent-skills · by K-Dense-AIQuery the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (Debt to the Penny), Daily Treasury Statements, Month…★ 46k GitHub starsFree

SkillAnalyze and engineer protein glycosylationGlycoengineering

K-Dense-AI/scientific-agent-skills · by K-Dense-AIAnalyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering t…★ 46k GitHub starsFree

SkillBuild, review, migrate, and safely plan MATLAB or GNU OctaveMATLAB and GNU Octave

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit…★ 46k GitHub starsFree

SkillOperator toolkit for nf-core/pacsomatic matched tumor-normal

K-Dense-AI/scientific-agent-skills · by K-Dense-AIOperator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-co…★ 46k GitHub starsFree

SkillBuild and analyze phylogenetic trees using MAFFT Phylogenetics

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evo…★ 46k GitHub starsFree

SkillRNA velocity analysis with scVeloscVelo — RNA Velocity Analysis

K-Dense-AI/scientific-agent-skills · by K-Dense-AIRNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify d…★ 46k GitHub starsFree

SkillSearch scientific papers and retrieve structuredBgpt paper search

K-Dense-AI/scientific-agent-skills · by K-Dense-AISearch scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including metho…★ 46k GitHub starsFree

SkillWorking with Brain Imaging Data Structure datasetsBrain Imaging Data Structure (BIDS)

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, m…★ 46k GitHub starsFree

SkillLocal document and PDF parsing that returns spatial textLiteParse — Local Document Parsing

K-Dense-AI/scientific-agent-skills · by K-Dense-AILocal document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; pr…★ 46k GitHub starsFree

SkillRun and analyze molecular dynamics simulations with OpenMM

K-Dense-AI/scientific-agent-skills · by K-Dense-AIRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and produc…★ 46k GitHub starsFree

SkillBuild with and use Pi, the minimal terminal coding harnessPi agent

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/settings/environment variables, creating Pi skills/extens…★ 46k GitHub starsFree

SkillHigh-performance genomic interval operationsPolars bio

K-Dense-AI/scientific-agent-skills · by K-Dense-AIHigh-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GF…★ 46k GitHub starsFree

SkillQuery the Precision Medicine Knowledge Graph for multiscalePrimeKG Knowledge Graph Skill

K-Dense-AI/scientific-agent-skills · by K-Dense-AIQuery the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.★ 46k GitHub starsFree

SkillPaste any email, proposal, or note someone wroteDHDNA Profiler — Cognitive Pattern Extraction

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPaste any email, proposal, or note someone wrote, and get back a plain-language read on how they think, what drives their decisions, and how they communicate.★ 46k GitHub starsFree

SkillPredict regulatory features, gene structureGenomic Intelligence — DNA Sequence Models

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPredict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU…★ 46k GitHub starsFree

SkillSubmit and manage protocols on Ginkgo Bioworks Cloud Lab Ginkgo cloud lab

K-Dense-AI/scientific-agent-skills · by K-Dense-AISubmit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs)…★ 46k GitHub starsFree

SkillBuild, run, and debug Nextflow data pipelines and nf-core

K-Dense-AI/scientific-agent-skills · by K-Dense-AIBuild, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, proce…★ 46k GitHub starsFree

SkillQuery the Cancer Dependency Map for cancer cell line geneDepMap — Cancer Dependency Map

K-Dense-AI/scientific-agent-skills · by K-Dense-AIQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifyi…★ 46k GitHub starsFree

SkillChat with your agent about projects, recommendationsPaperzilla

K-Dense-AI/scientific-agent-skills · by K-Dense-AIChat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper details,…★ 46k GitHub starsFree

SkillHand in a decision you're stuck onTough Decision Advisor: Every Angle Considered

K-Dense-AI/scientific-agent-skills · by K-Dense-AIHand in a decision you're stuck on. Get back a clear breakdown of every angle — the trade-offs, the risks, the blind spot, and a recommended path.★ 46k GitHub starsFree

SkillAutonomously improve a real artifact against an objectiveArbor — Autonomous Optimization via Hypothesis Tree Refinement

K-Dense-AI/scientific-agent-skills · by K-Dense-AIAutonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinemen…★ 46k GitHub starsFree

SkillEnd-to-end bulk RNA-seqBulk rnaseq

K-Dense-AI/scientific-agent-skills · by K-Dense-AIEnd-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCoun…★ 46k GitHub starsFree

SkillDesign experiments and studies BEFORE data isExperimental design

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDesign experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable. U…★ 46k GitHub starsFree

SkillQuery the 1000 Genomes Project datasetOneKGPd: Individual-Level Queries over the 1000 Genomes Project

K-Dense-AI/scientific-agent-skills · by K-Dense-AIQuery the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individua…★ 46k GitHub starsFree

SkillSearch and read full-text biomedical papersPaperclip CLI

K-Dense-AI/scientific-agent-skills · by K-Dense-AISearch and read full-text biomedical papers, FDA/PMDA/EMA regulatory documents, clinical trial registries, and UniProt/PDB/ChEMBL entries with the Paperclip CLI from GXL…★ 46k GitHub starsFree

SkillRun pathway and gene-set enrichment analysis on gene listsPathway enrichment

K-Dense-AI/scientific-agent-skills · by K-Dense-AIRun pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expr…★ 46k GitHub starsFree

SkillPharmacokinetic and pharmacodynamic modelling and

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orien…★ 46k GitHub starsFree

SkillAccess a collection of open-source molecular designTamarind Bio

K-Dense-AI/scientific-agent-skills · by K-Dense-AIAccess a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. T…★ 46k GitHub starsFree

SkillDesign custom laboratory hardware as parametric build123dLab hardware cad

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDesign custom laboratory hardware as parametric build123d models and export fabrication-ready STEP, STL, and DXF files - microfluidic chips and molds, optomechanical mou…★ 46k GitHub starsFree

SkillResolve free-text scientific labels to ontology term IDsOntology term resolution

K-Dense-AI/scientific-agent-skills · by K-Dense-AIResolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also look up prefixes in Bioregistr…★ 46k GitHub starsFree

SkillSample-size and statistical power calculations for planningStatistical Power & Sample Size

K-Dense-AI/scientific-agent-skills · by K-Dense-AISample-size and statistical power calculations for planning studies. Use whenever someone asks "how many subjects/samples/replicates do I need", wants an a priori power…★ 46k GitHub starsFree

SkillPlan, execute, and document validation, verificationAnalytical method validation

K-Dense-AI/scientific-agent-skills · by K-Dense-AIPlan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>,…★ 46k GitHub starsFree

SkillRetrieve ClinGen gene-disease validity assertionsFolklore variant evidence

K-Dense-AI/scientific-agent-skills · by K-Dense-AIRetrieve ClinGen gene-disease validity assertions for a public gene or disease, and review source-linked public evidence and literature for one supported GRCh38 germline…★ 46k GitHub starsFree

SkillConvert genomic intervals between coordinate conventionsGenomic coordinates

K-Dense-AI/scientific-agent-skills · by K-Dense-AIConvert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corr…★ 46k GitHub starsFree

SkillParticle Image Velocimetry analysis with OpenPIV

K-Dense-AI/scientific-agent-skills · by K-Dense-AIParticle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs, analyzing fluid dynamics or flow visualization experime…★ 46k GitHub starsFree

SkillQuery live pathogen genomic surveillance dataPathogen variant surveillance

K-Dense-AI/scientific-agent-skills · by K-Dense-AIQuery live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mut…★ 46k GitHub starsFree

SkillMultivariate severity assessment and humane endpointRELSA severity assessment and humane endpoint forecasting

K-Dense-AI/scientific-agent-skills · by K-Dense-AIMultivariate severity assessment and humane endpoint prediction for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcas…★ 46k GitHub starsFree

SkillTrack physical units and propagate measurement uncertaintyUncertainty and units

K-Dense-AI/scientific-agent-skills · by K-Dense-AITrack physical units and propagate measurement uncertainty in scientific calculations using pint and uncertainties. Use for unit conversion and dimensional checking, GUM…★ 46k GitHub starsFree

SkillWorking with Outpost Bio's open microbiome foundationWaypoint: Outpost Bio's Open Microbiome Foundation Models

K-Dense-AI/scientific-agent-skills · by K-Dense-AIUse when working with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas pretraining corpus…★ 46k GitHub starsFree

SkillRuns Cantera homogeneous chemical reactorsCantera: homogeneous ignition calculations

K-Dense-AI/scientific-agent-skills · by K-Dense-AIRuns Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kine…★ 46k GitHub starsFree

SkillEstimates intracellular metabolic fluxes from steady-stateCarbon-13 metabolic flux inference

K-Dense-AI/scientific-agent-skills · by K-Dense-AIEstimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multis…★ 46k GitHub starsFree

SkillRuns reproducible CellProfiler microscopy pipelinesCellProfiler quantitative microscopy

K-Dense-AI/scientific-agent-skills · by K-Dense-AIRuns reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/channel manifests, he…★ 46k GitHub starsFree

SkillOperates Fictiv , the on-demand manufacturing platformFictiv: quote, order and troubleshoot custom parts

K-Dense-AI/scientific-agent-skills · by K-Dense-AIOperates Fictiv (app.fictiv.com), the on-demand manufacturing platform, end to end in the user's browser. Covers uploading CAD parts, configuring process, material, fini…★ 46k GitHub starsFree

SkillAnalyzes flow cytometry data with FlowKit

K-Dense-AI/scientific-agent-skills · by K-Dense-AIAnalyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strategies, and supporte…★ 46k GitHub starsFree

SkillAnalyzes pooled CRISPR screen FASTQ reads and guide-countMAGeCK pooled-screen analysis

K-Dense-AI/scientific-agent-skills · by K-Dense-AIAnalyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and library QC, and produces…★ 46k GitHub starsFree

SkillSolves seawater carbonate chemistry with PyCO2SYSMarine carbonate chemistry

K-Dense-AI/scientific-agent-skills · by K-Dense-AISolves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired total alkalinity, diss…★ 46k GitHub starsFree

SkillProcesses calibrated one-dimensional complex NMRnmrglue: calibrated 1D FID processing

K-Dense-AI/scientific-agent-skills · by K-Dense-AIProcesses calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration regions. Use for raw 1D…★ 46k GitHub starsFree

SkillDesigns and audits PCR and RT-qPCR primers with Primer3Primer design and specificity

K-Dense-AI/scientific-agent-skills · by K-Dense-AIDesigns and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coo…★ 46k GitHub starsFree

SkillSimulates lithium-ion battery chargePyBaMM battery experiments

K-Dense-AI/scientific-agent-skills · by K-Dense-AISimulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, checks mesh and solver sensitivity, and compares pred…★ 46k GitHub starsFree

SkillComputes finite-temperature CALPHAD equilibriapycalphad: TDB equilibrium calculations

K-Dense-AI/scientific-agent-skills · by K-Dense-AIComputes finite-temperature CALPHAD equilibria, phase fractions, and phase compositions from thermodynamic TDB databases using pycalphad. Use for alloy phase stability,…★ 46k GitHub starsFree

SkillProcesses paired-end 16S amplicon reads into QIIME 2 ASVsQIIME 2 paired-end 16S amplicons

K-Dense-AI/scientific-agent-skills · by K-Dense-AIProcesses paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer orientation diagnostics,…★ 46k GitHub starsFree

SkillValidates and executes RELION single-particle cryo-EMRELION single-particle refinement

K-Dense-AI/scientific-agent-skills · by K-Dense-AIValidates and executes RELION single-particle cryo-EM refinement and half-map postprocessing. Supports STAR optics/acquisition checks, particle-stack consistency, gold-s…★ 46k GitHub starsFree

SkillSimulates biochemical kinetic models from SBML or AntimonyTellurium kinetic experiments

K-Dense-AI/scientific-agent-skills · by K-Dense-AISimulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter perturbations, and expo…★ 46k GitHub starsFree

SkillConverts neuroscience acquisition data to NeurodataValidated NWB conversion

K-Dense-AI/scientific-agent-skills · by K-Dense-AIConverts neuroscience acquisition data to Neurodata Without Borders files with NeuroConv and PyNWB, preserves metadata and timebases, checks evidence-based clock alignme…★ 46k GitHub starsFree