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k-dense-ai/scientific-agent-skills

skills.sh installs
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skills
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Install

$ npx -y skills add k-dense-ai/scientific-agent-skills --agent claude-code

Installs into .claude/skills of the current project.

Skills

1k-dense-ai avatarscientific-writingk-dense-ai/scientific-agent-skillsDraft, revise, and audit scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confident2.6Kskills.sh installs
2k-dense-ai avatarscientific-visualizationk-dense-ai/scientific-agent-skillsCreate and audit truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use for figure design, multi-panel layouts, unc2.6Kskills.sh installs
3k-dense-ai avatarscientific-critical-thinkingk-dense-ai/scientific-agent-skillsEvaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading f2.5Kskills.sh installs
4k-dense-ai avatarliterature-reviewk-dense-ai/scientific-agent-skillsConduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be us2.5Kskills.sh installs
5k-dense-ai avatarscientific-brainstormingk-dense-ai/scientific-agent-skillsFacilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial rev2.4Kskills.sh installs
6k-dense-ai avatarstatistical-analysisk-dense-ai/scientific-agent-skillsGuided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted repo2.4Kskills.sh installs
7k-dense-ai avatarpaper-lookupk-dense-ai/scientific-agent-skillsSearch 11 academic literature APIs for papers, preprints, citations, and open-access full text, and return results with reproducible provenance. Covers PubMed, 2.4Kskills.sh installs
8k-dense-ai avatarcitation-managementk-dense-ai/scientific-agent-skillsComprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, 2.4Kskills.sh installs
9k-dense-ai avatarpeer-reviewk-dense-ai/scientific-agent-skillsPrepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized review of scientific manuscripts, protocols,2.3Kskills.sh installs
10k-dense-ai avatarmatplotlibk-dense-ai/scientific-agent-skillsLow-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating wit2.3Kskills.sh installs
11k-dense-ai avatarscientific-slidesk-dense-ai/scientific-agent-skillsBuild slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, 2.3Kskills.sh installs
12k-dense-ai avatarscikit-learnk-dense-ai/scientific-agent-skillsMachine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensi2.3Kskills.sh installs
13k-dense-ai avatarscientific-schematicsk-dense-ai/scientific-agent-skillsCreate publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Only regenerate2.3Kskills.sh installs
14k-dense-ai avatarexploratory-data-analysisk-dense-ai/scientific-agent-skillsPerform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ,2.3Kskills.sh installs
15k-dense-ai avatarstatsmodelsk-dense-ai/scientific-agent-skillsStatistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and infere2.3Kskills.sh installs
16k-dense-ai avatarmarkitdownk-dense-ai/scientific-agent-skillsConvert heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion. Covers safe local conv2.2Kskills.sh installs
17k-dense-ai avatarhypothesis-generationk-dense-ai/scientific-agent-skillsFormulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measureme2.2Kskills.sh installs
18k-dense-ai avatarmarkdown-mermaid-writingk-dense-ai/scientific-agent-skillsComprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based 2.2Kskills.sh installs
19k-dense-ai avatarseabornk-dense-ai/scientific-agent-skillsStatistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaul2.2Kskills.sh installs
20k-dense-ai avatardatabase-lookupk-dense-ai/scientific-agent-skillsQuery documented public database APIs with explicit endpoints, filters, pagination, and provenance. Use when a scientific, regulatory, financial, or other datab2.2Kskills.sh installs
21k-dense-ai avatarscholar-evaluationk-dense-ai/scientific-agent-skillsProvide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quali2.2Kskills.sh installs
22k-dense-ai avatarpolarsk-dense-ai/scientific-agent-skillsHigh-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization, par2.2Kskills.sh installs
23k-dense-ai avatarlatex-postersk-dense-ai/scientific-agent-skillsCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientifi2.2Kskills.sh installs
24k-dense-ai avatarpptx-postersk-dense-ai/scientific-agent-skillsCreate and audit editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets. Use when the requested deliverable 2.2Kskills.sh installs
25k-dense-ai avatarbgpt-paper-searchk-dense-ai/scientific-agent-skillsSearch scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper includ2.2Kskills.sh installs
26k-dense-ai avatarresearch-grantsk-dense-ai/scientific-agent-skillsWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts2.1Kskills.sh installs
27k-dense-ai avatarsympyk-dense-ai/scientific-agent-skillsUse when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code generation via lambdify/LaTeX. Prefer Nu2.1Kskills.sh installs
28k-dense-ai avatarpytorch-lightningk-dense-ai/scientific-agent-skillsDeep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement da2.1Kskills.sh installs
29k-dense-ai avatarnetworkxk-dense-ai/scientific-agent-skillsCreate, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph algorit2.1Kskills.sh installs
30k-dense-ai avataraeonk-dense-ai/scientific-agent-skillsThis skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation,2.1Kskills.sh installs
31k-dense-ai avatartransformersk-dense-ai/scientific-agent-skillsHugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimodal tas2.1Kskills.sh installs
32k-dense-ai avatarshapk-dense-ai/scientific-agent-skillsExplain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and validating feature attributions, handling2.1Kskills.sh installs
33k-dense-ai avatarpyzoterok-dense-ai/scientific-agent-skillsInteract with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachm2.1Kskills.sh installs
34k-dense-ai avatargenerate-imagek-dense-ai/scientific-agent-skillsGenerate or edit images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos, illustrations, artwor2.1Kskills.sh installs
35k-dense-ai avatardaskk-dense-ai/scientific-agent-skillsDistributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best f2.1Kskills.sh installs
36k-dense-ai avatarinfographicsk-dense-ai/scientific-agent-skillsCreate professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Integrates research-lookup 2.1Kskills.sh installs
37k-dense-ai avatarmarket-research-reportsk-dense-ai/scientific-agent-skillsBuild evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evi2.1Kskills.sh installs
38k-dense-ai avatarmatlabk-dense-ai/scientific-agent-skillsBuild, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and2.1Kskills.sh installs
39k-dense-ai avatarget-available-resourcesk-dense-ai/scientific-agent-skillsDetect host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a cle2.1Kskills.sh installs
40k-dense-ai avataroptimize-for-gpuk-dense-ai/scientific-agent-skillsGPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster. Use for CUDA/GPU optimization; CPU-bound NumPy, SciPy, 2.1Kskills.sh installs
41k-dense-ai avatarpymck-dense-ai/scientific-agent-skillsBayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming2.1Kskills.sh installs
42k-dense-ai avatarumap-learnk-dense-ai/scientific-agent-skillsUse UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP, and2.1Kskills.sh installs
43k-dense-ai avatarparallel-webk-dense-ai/scientific-agent-skillsUse Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and recurring web monitoring. Best for requests th2.1Kskills.sh installs
44k-dense-ai avatarvenue-templatesk-dense-ai/scientific-agent-skillsPrepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting guidance and bundled LaTeX scaffolds. Use 2.1Kskills.sh installs
45k-dense-ai avatarscikit-survivalk-dense-ai/scientific-agent-skillsBuild, evaluate, and audit right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model selection, prob2.1Kskills.sh installs
46k-dense-ai avataropen-notebookk-dense-ai/scientific-agent-skillsSelf-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, 2.1Kskills.sh installs
47k-dense-ai avatartorch-geometrick-dense-ai/scientific-agent-skillsPyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor s2.1Kskills.sh installs
48k-dense-ai avatarbiopythonk-dense-ai/scientific-agent-skillsComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bi2.1Kskills.sh installs
49k-dense-ai avatarresearch-lookupk-dense-ai/scientific-agent-skillsCompile current scholarly evidence for a scientific manuscript or research brief. Use when the user explicitly asks to gather literature, references, background2.1Kskills.sh installs
50k-dense-ai avatartimesfm-forecastingk-dense-ai/scientific-agent-skillsZero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without t2.1Kskills.sh installs
51k-dense-ai avatargeopandask-dense-ai/scientific-agent-skillsGuidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.2.1Kskills.sh installs
52k-dense-ai avatarstable-baselines3k-dense-ai/scientific-agent-skillsProduction-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototypin2.1Kskills.sh installs
53k-dense-ai avatarconsciousness-councilk-dense-ai/scientific-agent-skillsRun a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, n2.1Kskills.sh installs
54k-dense-ai avatarsimpyk-dense-ai/scientific-agent-skillsBuild, inspect, test, and analyze bounded process-based discrete-event simulations with SimPy, including events, resources, interrupts, monitoring, replications2.1Kskills.sh installs
55k-dense-ai avatarpymook-dense-ai/scientific-agent-skillsMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimi2.1Kskills.sh installs
56k-dense-ai avatarscikit-biok-dense-ai/scientific-agent-skillsBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick 2.1Kskills.sh installs
57k-dense-ai avatargeomasterk-dense-ai/scientific-agent-skillsComprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Suppo2.1Kskills.sh installs
58k-dense-ai avatarwhat-if-oraclek-dense-ai/scientific-agent-skillsRun structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use when the user a2.1Kskills.sh installs
59k-dense-ai avatarhypogenick-dense-ai/scientific-agent-skillsPlans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text datasets. Use for the `hypogenic` package, its 2.1Kskills.sh installs
60k-dense-ai avatarbioservicesk-dense-ai/scientific-agent-skillsUnified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consis2.1Kskills.sh installs
61k-dense-ai avataranndatak-dense-ai/scientific-agent-skillsData structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data for2.1Kskills.sh installs
62k-dense-ai avatarclinical-reportsk-dense-ai/scientific-agent-skillsCreate safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only2Kskills.sh installs
63k-dense-ai avatarclinical-decision-supportk-dense-ai/scientific-agent-skillsPrepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts.2Kskills.sh installs
64k-dense-ai avatarggetk-dense-ai/scientific-agent-skillsFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichmen2Kskills.sh installs
65k-dense-ai avatarrdkitk-dense-ai/scientific-agent-skillsCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generatio2Kskills.sh installs
66k-dense-ai avatarmodalk-dense-ai/scientific-agent-skillsModal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accelerated2Kskills.sh installs
67k-dense-ai avatarscanpyk-dense-ai/scientific-agent-skillsStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visua2Kskills.sh installs
68k-dense-ai avatarastropyk-dense-ai/scientific-agent-skillsCore Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WC2Kskills.sh installs
69k-dense-ai avatarcellxgene-censusk-dense-ai/scientific-agent-skillsQuery the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metada2Kskills.sh installs
70k-dense-ai avatarpydicomk-dense-ai/scientific-agent-skillsUse pydicom to read, inspect, write, transform, and safely preflight local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compress2Kskills.sh installs
71k-dense-ai avatardatamolk-dense-ai/scientific-agent-skillsPythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, 2Kskills.sh installs
72k-dense-ai avatardeeptoolsk-dense-ai/scientific-agent-skillsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualizati2Kskills.sh installs
73k-dense-ai avatardeepchemk-dense-ai/scientific-agent-skillsMolecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive 2Kskills.sh installs
74k-dense-ai avatarpufferlibk-dense-ai/scientific-agent-skillsVersion-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review. Use2Kskills.sh installs
75k-dense-ai avatarbenchling-integrationk-dense-ai/scientific-agent-skillsBenchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when aut2Kskills.sh installs
76k-dense-ai avatarvaexk-dense-ai/scientific-agent-skillsUse this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations2Kskills.sh installs
77k-dense-ai avataradaptyvk-dense-ai/scientific-agent-skillsHow to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mention2Kskills.sh installs
78k-dense-ai avatararboretok-dense-ai/scientific-agent-skillsInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA2Kskills.sh installs
79k-dense-ai avatarmolecular-dynamicsk-dense-ai/scientific-agent-skillsRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization a2Kskills.sh installs
80k-dense-ai avatarpydeseq2k-dense-ai/scientific-agent-skillsDifferential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visuali2Kskills.sh installs
81k-dense-ai avatarpymatgenk-dense-ai/scientific-agent-skillsAnalyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs, including local phase diagrams, symmetry 2Kskills.sh installs
82k-dense-ai avatartorchdrugk-dense-ai/scientific-agent-skillsBuild and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, pr2Kskills.sh installs
83k-dense-ai avatarfluidsimk-dense-ai/scientific-agent-skillsPlan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks.2Kskills.sh installs
84k-dense-ai avatarimaging-data-commonsk-dense-ai/scientific-agent-skillsQuery and download public cancer imaging data from NCI Imaging Data Commons. Invoke for any question about IDC collections, cancer imaging datasets, DICOM data 2Kskills.sh installs
85k-dense-ai avatarpaperzillak-dense-ai/scientific-agent-skillsChat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper2Kskills.sh installs
86k-dense-ai avatarzarr-pythonk-dense-ai/scientific-agent-skillsChunked 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 scientif2Kskills.sh installs
87k-dense-ai avataresmk-dense-ai/scientific-agent-skillsUse when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.2Kskills.sh installs
88k-dense-ai avatarpyhealthk-dense-ai/scientific-agent-skillsBuild clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot)2Kskills.sh installs
89k-dense-ai avatarscvi-toolsk-dense-ai/scientific-agent-skillsDeep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertain2Kskills.sh installs
90k-dense-ai avatarneurokit2k-dense-ai/scientific-agent-skillsUse NeuroKit2 to build or audit reproducible research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, vari2Kskills.sh installs
91k-dense-ai avatardhdna-profilerk-dense-ai/scientific-agent-skillsExtract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style2Kskills.sh installs
92k-dense-ai avatarmedchemk-dense-ai/scientific-agent-skillsMedicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity m2Kskills.sh installs
93k-dense-ai avatarmolfeatk-dense-ai/scientific-agent-skillsMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular M2Kskills.sh installs
94k-dense-ai avatarcobrapyk-dense-ai/scientific-agent-skillsConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.2Kskills.sh installs
95k-dense-ai avatardepmapk-dense-ai/scientific-agent-skillsQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for 2Kskills.sh installs
96k-dense-ai avatardiffdockk-dense-ai/scientific-agent-skillsDiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual scre2Kskills.sh installs
97k-dense-ai avatarpysamk-dense-ai/scientific-agent-skillsPython/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, inclu2Kskills.sh installs
98k-dense-ai avatarcirqk-dense-ai/scientific-agent-skillsGoogle quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experimen2Kskills.sh installs
99k-dense-ai avatarpathmlk-dense-ai/scientific-agent-skillsUse PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and QC pipelines, manage h5path data, quantify 2Kskills.sh installs
100k-dense-ai avatartreatment-plansk-dense-ai/scientific-agent-skillsFormat and structurally validate local treatment-plan documentation after clinical decisions have already been supplied and verified by authorized licensed prof2Kskills.sh installs
101k-dense-ai avataretetoolkitk-dense-ai/scientific-agent-skillsAnalyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pat2Kskills.sh installs
102k-dense-ai avatargenimlk-dense-ai/scientific-agent-skillsUse Geniml for audited local genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer compatibi2Kskills.sh installs
103k-dense-ai avatarpennylanek-dense-ai/scientific-agent-skillsHardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical model2Kskills.sh installs
104k-dense-ai avatarflowiok-dense-ai/scientific-agent-skillsRead, 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 e2Kskills.sh installs
105k-dense-ai avatarlabarchive-integrationk-dense-ai/scientific-agent-skillsSecurely integrate with the official LabArchives ELN REST-like API and Inventory API v1. Use for regional endpoint selection, signed-request construction, user 2Kskills.sh installs
106k-dense-ai avatarpytdck-dense-ai/scientific-agent-skillsUse Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset access, task-aware splits, evaluator metrics, benchmark 2Kskills.sh installs
107k-dense-ai avatarlamindbk-dense-ai/scientific-agent-skillsUse when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, l2Kskills.sh installs
108k-dense-ai avatarphylogeneticsk-dense-ai/scientific-agent-skillsBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree2Kskills.sh installs
109k-dense-ai avatarscvelok-dense-ai/scientific-agent-skillsRNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and i2Kskills.sh installs
110k-dense-ai avatarusfiscaldatak-dense-ai/scientific-agent-skillsQuery 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 Statemen2Kskills.sh installs
111k-dense-ai avatarqiskitk-dense-ai/scientific-agent-skillsBuild, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator2Kskills.sh installs
112k-dense-ai avatargtarsk-dense-ai/scientific-agent-skillsUse Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase 2Kskills.sh installs
113k-dense-ai avatarmatchmsk-dense-ai/scientific-agent-skillsProcess, clean, compare, and search tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, libra2Kskills.sh installs
114k-dense-ai avatarprotocolsio-integrationk-dense-ai/scientific-agent-skillsRead, validate, and safely export protocols.io data with current official REST/MCP contracts, or create non-executing mutation plans. The bundled client makes b2Kskills.sh installs
115k-dense-ai avatarhistolabk-dense-ai/scientific-agent-skillsLightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images. Be2Kskills.sh installs
116k-dense-ai avatarpolars-biok-dense-ai/scientific-agent-skillsHigh-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/V2Kskills.sh installs
117k-dense-ai avatarneuropixels-analysisk-dense-ai/scientific-agent-skillsAnalyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction2Kskills.sh installs
118k-dense-ai avatarpyopenmsk-dense-ai/scientific-agent-skillsComplete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free and is2Kskills.sh installs
119k-dense-ai avatardnanexus-integrationk-dense-ai/scientific-agent-skillsBuild and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus 2Kskills.sh installs
120k-dense-ai avatarlatchbio-integrationk-dense-ai/scientific-agent-skillsBuild, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic exec2Kskills.sh installs
121k-dense-ai avatarqutipk-dense-ai/scientific-agent-skillsSimulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. U2Kskills.sh installs
122k-dense-ai avatarrowank-dense-ai/scientific-agent-skillsRowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tauto2Kskills.sh installs
123k-dense-ai avataromero-integrationk-dense-ai/scientific-agent-skillsSecurely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and d2Kskills.sh installs
124k-dense-ai avataropentrons-integrationk-dense-ai/scientific-agent-skillsAuthor, review, migrate, simulate, and troubleshoot official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for robot-specific liquid 2Kskills.sh installs
125k-dense-ai avatartiledbvcfk-dense-ai/scientific-agent-skillsEfficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel quer2Kskills.sh installs
126k-dense-ai avatarpylabrobotk-dense-ai/scientific-agent-skillsDevelop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Use for PyLabRobot protoc2Kskills.sh installs
127k-dense-ai avatarprimekgk-dense-ai/scientific-agent-skillsQuery the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.2Kskills.sh installs
128k-dense-ai avatarglycoengineeringk-dense-ai/scientific-agent-skillsAnalyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengi2Kskills.sh installs
129k-dense-ai avatarginkgo-cloud-labk-dense-ai/scientific-agent-skillsSubmit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Car2Kskills.sh installs
130k-dense-ai avatarhugging-sciencek-dense-ai/scientific-agent-skillsUse when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, en1.9Kskills.sh installs
131k-dense-ai avatarautoskillk-dense-ai/scientific-agent-skillsObserve the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or comp1.9Kskills.sh installs
132k-dense-ai avatarpdfk-dense-ai/scientific-agent-skillsUse this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple P1.8Kskills.sh installs
133k-dense-ai avatardocxk-dense-ai/scientific-agent-skillsUse this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any 1.8Kskills.sh installs
134k-dense-ai avatarpptxk-dense-ai/scientific-agent-skillsUse this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentat1.8Kskills.sh installs
135k-dense-ai avatarexa-searchk-dense-ai/scientific-agent-skillsWeb 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. Cover1.8Kskills.sh installs
136k-dense-ai avatarxlsxk-dense-ai/scientific-agent-skillsCreate, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, fin1.8Kskills.sh installs
137k-dense-ai avatariso-13485-certificationk-dense-ai/scientific-agent-skillsPrepare and structurally review ISO 13485 QMS scope, controlled documentation, and local evidence manifests. Use for ISO 13485 certification-readiness documenta915skills.sh installs