k-dense-ai/scientific-agent-skills
178 instruction files for AI agents, collected from k-dense-ai/scientific-agent-skills. Install any of them at an exact version with mdr add k-dense-ai/scientific-agent-skills/<name>.
git:20261001.f7a50ed · audit A · 56,497 stars
13c-metabolic-flux SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/13c-metabolic-flux/SKILL.md · Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom…
v1.2 · audit A · 56,497 stars
adaptyv SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/adaptyv/SKILL.md · Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit…
v1.5 · audit A · 56,497 stars
aeon SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/aeon/SKILL.md · This skill should be used for time series machine learning tasks including classification, regression, clustering…
v1.3 · audit A · 56,497 stars
alphagenome SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/alphagenome/SKILL.md · Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18…
v1.2 · audit A · 56,497 stars
analytical-method-validation SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/analytical-method-validation/SKILL.md · Plans, executes, and documents validation, verification, and transfer of analytical procedures under the governing…
v2.0 · audit A · 56,497 stars
anndata SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/anndata/SKILL.md · Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem…
v1.4 · audit A · 56,497 stars
arbor SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/arbor/SKILL.md · Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training…
v1.6 · audit A · 56,497 stars
arboreto SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/arboreto/SKILL.md · Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2…
v1.3 · audit A · 56,497 stars
astropy SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/astropy/SKILL.md · Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities…
v1.5 · audit A · 56,497 stars
autoskill SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/autoskill/SKILL.md · Analyzes user-requested Screenpipe history windows to detect repeated research workflows, match existing scientific…
v1.6 · audit A · 56,497 stars
benchling-integration SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/benchling-integration/SKILL.md · Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps…
v1.7 · audit A · 56,497 stars
bgpt-paper-search SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/bgpt-paper-search/SKILL.md · Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including…
v1.3 · audit A · 56,497 stars
bids SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/bids/SKILL.md · Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets. Supports organizing…
v1.3 · audit A · 56,497 stars
biopython SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/biopython/SKILL.md · Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and…
v1.5 · audit A · 56,497 stars
bioservices SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/bioservices/SKILL.md · Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem…
v1.7 · audit A · 56,497 stars
bulk-rnaseq SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/bulk-rnaseq/SKILL.md · Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers…
v2.0 · audit A · 56,497 stars
cantera SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/cantera/SKILL.md · Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks…
v1.1 · audit A · 56,497 stars
cellprofiler SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/cellprofiler/SKILL.md · Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence…
v1.1 · audit A · 56,497 stars
cellxgene-census SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/cellxgene-census/SKILL.md · Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use…
v1.5 · audit A · 56,497 stars
cirq SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/cirq/SKILL.md · Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or…
v1.3 · audit A · 56,497 stars
citation-management SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/citation-management/SKILL.md · Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers…
v2.3 · audit A · 56,497 stars
clinical-decision-support SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/clinical-decision-support/SKILL.md · Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival…
v2.4 · audit A · 56,497 stars
clinical-reports SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/clinical-reports/SKILL.md · Creates safety-bounded draft structures and runs local deterministic checks for clinical case, diagnostic, trial…
v2.3 · audit A · 56,497 stars
cobrapy SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/cobrapy/SKILL.md · Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling…
v1.5 · audit A · 56,497 stars
consciousness-council SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/consciousness-council/SKILL.md · Structures a multi-perspective council exercise for decisions, research trade-offs, and creative challenges. Simulates…
v1.2 · audit A · 56,497 stars
dask SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/dask/SKILL.md · Scales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask. Covers…
v1.4 · audit A · 56,497 stars
database-lookup SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/database-lookup/SKILL.md · Queries documented public database APIs with explicit endpoints, filters, pagination, and provenance. Used when a…
v1.8 · audit B · 56,497 stars
datalad SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/datalad/SKILL.md · Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational…
v1.2 · audit A · 56,497 stars
datamol SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/datamol/SKILL.md · Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery…
v1.4 · audit A · 56,497 stars
deepchem SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/deepchem/SKILL.md · Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold…
v2.0 · audit A · 56,497 stars
deepspot-m SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/deepspot-m/SKILL.md · Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted…
v1.2 · audit A · 56,497 stars
deeptools SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/deeptools/SKILL.md · NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks)…
v2.0 · audit A · 56,497 stars
depmap SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/depmap/SKILL.md · Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model…
v1.2 · audit A · 56,497 stars
dhdna-profiler SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/dhdna-profiler/SKILL.md · Applies the DHDNA framework as an exploratory rubric for reasoning and writing patterns in supplied text. Used for…
v2.0 · audit A · 56,497 stars
diffdock SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/diffdock/SKILL.md · Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2…
v1.6 · audit A · 56,497 stars
dnanexus-integration SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/dnanexus-integration/SKILL.md · Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows…
v2.3 · audit A · 56,497 stars
esm SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/esm/SKILL.md · Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to…
v2.0 · audit A · 56,497 stars
etetoolkit SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/etetoolkit/SKILL.md · Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4…
v3.0 · audit A · 56,497 stars
exa-search SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/exa-search/SKILL.md · Searches scientific and technical web content with Exa and extracts page or PDF text from URLs in batches. Supports…
v1.4 · audit A · 56,497 stars
experimental-design SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/experimental-design/SKILL.md · Designs experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out…
v1.5 · audit A · 56,497 stars
exploratory-data-analysis SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/exploratory-data-analysis/SKILL.md · Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON…
v1.4 · audit A · 56,497 stars
fictiv SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/fictiv/SKILL.md · Operates Fictiv (app.fictiv.com), the on-demand manufacturing platform, end to end in the user's browser. Covers…
v1.3 · audit A · 56,497 stars
flowio SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/flowio/SKILL.md · Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS…
v2.3 · audit A · 56,497 stars
flowkit SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/flowkit/SKILL.md · Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms…
v1.1 · audit A · 56,497 stars
fluidsim SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/fluidsim/SKILL.md · Plans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with…
v1.4 · audit A · 56,497 stars
folklore-variant-evidence SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/folklore-variant-evidence/SKILL.md · Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public…
v1.2 · audit A · 56,497 stars
generate-image SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/generate-image/SKILL.md · Generates or edits images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image…
v3.3 · audit A · 56,497 stars
geniml SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/geniml/SKILL.md · Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or…
v1.4 · audit A · 56,497 stars
genomic-coordinates SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/genomic-coordinates/SKILL.md · Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects…
v1.3 · audit A · 56,497 stars
genomic-intelligence SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/genomic-intelligence/SKILL.md · Predicts regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's…
v1.4 · audit A · 56,497 stars
geomaster SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/geomaster/SKILL.md · Supports geospatial research workflows for remote sensing, vector and raster GIS, spatial statistics, terrain and…
v1.5 · audit A · 56,497 stars
geopandas SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/geopandas/SKILL.md · Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial…
v1.4 · audit A · 56,497 stars
get-available-resources SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/get-available-resources/SKILL.md · Detects host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks…
v1.5 · audit A · 56,497 stars
gget SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/gget/SKILL.md · Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral…
v1.7 · audit A · 56,497 stars
ginkgo-cloud-lab SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/ginkgo-cloud-lab/SKILL.md · Guides protocol selection, input preparation, pricing checks, and browser ordering on Ginkgo Bioworks Cloud Lab…
v2.3 · audit A · 56,497 stars
glycoengineering SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/glycoengineering/SKILL.md · Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich…
v1.4 · audit A · 56,497 stars
gtars SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/gtars/SKILL.md · Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage…
v1.5 · audit A · 56,497 stars
histolab SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/histolab/SKILL.md · Extracts and preprocesses whole-slide histology image tiles with Histolab. Use for WSI inspection, tissue masks…
v1.5 · audit A · 56,497 stars
hugging-science SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/hugging-science/SKILL.md · Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog…
v1.5 · audit A · 56,497 stars
hypogenic SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/hypogenic/SKILL.md · Plans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text…
v1.4 · audit A · 56,497 stars
hypothesis-generation SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/hypothesis-generation/SKILL.md · Formulates evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational…
v2.4 · audit A · 56,497 stars
imaging-data-commons SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/imaging-data-commons/SKILL.md · Queries and downloads public cancer imaging data from NCI Imaging Data Commons. Supports IDC collection discovery…
v1.8 · audit A · 56,497 stars
infographics SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/infographics/SKILL.md · Creates and reviews infographics with Nano Banana 2 via OpenRouter. Use for statistical summaries, timelines…
v1.10 · audit A · 56,497 stars
iso-standards-readiness SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/iso-standards-readiness/SKILL.md · Prepares and structurally reviews readiness evidence for ISO management-system and laboratory-competence standards -…
v1.3 · audit A · 56,497 stars
lab-hardware-cad SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/lab-hardware-cad/SKILL.md · Designs custom laboratory hardware as parametric build123d models and exports fabrication artifacts as STEP, STL, and…
v1.5 · audit A · 56,497 stars
labarchive-integration SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/labarchive-integration/SKILL.md · Integrates with the official LabArchives ELN REST-like API and Inventory API v1. Supports regional endpoint selection…
v1.4 · audit A · 56,497 stars
lamindb SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/lamindb/SKILL.md · Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema…
v2.0 · audit A · 56,497 stars
latchbio-integration SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/latchbio-integration/SKILL.md · Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and…
v2.3 · audit A · 56,497 stars
latex-posters SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/latex-posters/SKILL.md · Creates research posters in LaTeX using beamerposter, tikzposter, or baposter. Use for conference posters, academic…
v1.10 · audit A · 56,497 stars
liteparse SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/liteparse/SKILL.md · Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX…
v1.6 · audit A · 56,497 stars
literature-review SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/literature-review/SKILL.md · Conducts systematic, scoping, and narrative literature reviews using PubMed, arXiv, bioRxiv, Semantic Scholar, and…
v1.11 · audit A · 56,497 stars
mageck SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/mageck/SKILL.md · Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and…
v1.1 · audit A · 56,497 stars
marine-carbonate-chemistry SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/marine-carbonate-chemistry/SKILL.md · Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine…
v1.1 · audit A · 56,497 stars
markdown-mermaid-writing SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/markdown-mermaid-writing/SKILL.md · Writes scientific Markdown documentation and Mermaid diagrams for workflows, relationships, timelines, and schemas…
v1.3 · audit A · 56,497 stars
market-research-reports SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/market-research-reports/SKILL.md · Builds evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for…
v1.5 · audit A · 56,497 stars
markitdown SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/markitdown/SKILL.md · Converts heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and…
v2.5 · audit A · 56,497 stars
matchms SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/matchms/SKILL.md · Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata…
v2.3 · audit A · 56,497 stars
matlab SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/matlab/SKILL.md · Builds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows. Use for arrays, tabular/time data…
v1.4 · audit A · 56,497 stars
matplotlib SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/matplotlib/SKILL.md · Creates and customizes scientific plots with Matplotlib. Used for fine-grained control over plot elements, novel plot…
v1.4 · audit A · 56,497 stars
medchem SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/medchem/SKILL.md · Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural…
v1.4 · audit A · 56,497 stars
modal SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/modal/SKILL.md · Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or…
v1.5 · audit A · 56,497 stars
molecular-dynamics SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/molecular-dynamics/SKILL.md · Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems…
v1.3 · audit A · 56,497 stars
molfeat SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/molfeat/SKILL.md · Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers…
v2.0 · audit A · 56,497 stars
ncats-arax SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/ncats-arax/SKILL.md · Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned…
v1.2 · audit A · 56,497 stars
networkx SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/networkx/SKILL.md · Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with…
v1.4 · audit A · 56,497 stars
neurokit2 SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/neurokit2/SKILL.md · Builds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval…
v1.4 · audit A · 56,497 stars
neuropixels-analysis SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/neuropixels-analysis/SKILL.md · Analyzes Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB…
v2.6 · audit A · 56,497 stars
nextflow SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/nextflow/SKILL.md · Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. Use for Nextflow, nf-core, .nf files…
v1.4 · audit A · 56,497 stars
nmrglue SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/nmrglue/SKILL.md · Processes calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak…
v1.1 · audit A · 56,497 stars
nwb-conversion SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/nwb-conversion/SKILL.md · Converts neuroscience acquisition data to Neurodata Without Borders files with NeuroConv and PyNWB, preserves metadata…
v1.1 · audit A · 56,497 stars
omero-integration SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/omero-integration/SKILL.md · Inspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables…
v1.6 · audit A · 56,497 stars
onekgpd SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/onekgpd/SKILL.md · Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual…
v1.4 · audit A · 56,497 stars
ontology-term-resolution SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/ontology-term-resolution/SKILL.md · Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup…
v1.4 · audit A · 56,497 stars
open-notebook SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/open-notebook/SKILL.md · Organizes research with the self-hosted Open Notebook alternative to NotebookLM. Supports source ingestion (PDFs, web…
v1.5 · audit A · 56,497 stars
openpiv SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/openpiv/SKILL.md · Performs Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image…
v1.3 · audit A · 56,497 stars
opentrons-integration SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/opentrons-integration/SKILL.md · Authors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex…
v2.3 · audit A · 56,497 stars
optimize-for-gpu SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/optimize-for-gpu/SKILL.md · GPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster. Use for…
v1.6 · audit A · 56,497 stars
pacsomatic SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pacsomatic/SKILL.md · Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs…
v1.4 · audit A · 56,497 stars
paper-lookup SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/paper-lookup/SKILL.md · Searches 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA…
v2.4 · audit A · 56,497 stars
paperclip SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/paperclip/SKILL.md · Searches and reads biomedical papers, FDA/PMDA/EMA documents, clinical trials, and protein records with the GXL…
v1.5 · audit A · 56,497 stars
paperzilla SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/paperzilla/SKILL.md · Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz…
v1.2 · audit A · 56,497 stars
parallel-web SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/parallel-web/SKILL.md · Uses Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and…
v1.5 · audit A · 56,497 stars
pathml SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pathml/SKILL.md · Supports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path…
v1.4 · audit A · 56,497 stars
pathogen-variant-surveillance SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pathogen-variant-surveillance/SKILL.md · Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence…
v1.3 · audit A · 56,497 stars
pathway-enrichment SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pathway-enrichment/SKILL.md · Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used…
v1.3 · audit A · 56,497 stars
peer-review SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/peer-review/SKILL.md · Prepares evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Supports authorized…
v2.4 · audit B · 56,497 stars
pennylane SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pennylane/SKILL.md · Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows…
v2.0 · audit A · 56,497 stars
phylogenetics SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/phylogenetics/SKILL.md · Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with…
v1.5 · audit A · 56,497 stars
pi-agent SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pi-agent/SKILL.md · Builds with and operates Pi, the minimal terminal coding harness. Use for installing Pi, configuring…
v1.6 · audit A · 56,497 stars
pkpd-modeling SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pkpd-modeling/SKILL.md · Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population…
v2.0 · audit A · 56,497 stars
polars-bio SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/polars-bio/SKILL.md · Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads…
v1.3 · audit A · 56,497 stars
polars SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/polars/SKILL.md · High-performance DataFrame library for Python ETL, analytics, and pandas migration. It supports expression-based data…
v1.4 · audit A · 56,497 stars
pptx-posters SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pptx-posters/SKILL.md · Creates and audits editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and…
v2.4 · audit A · 56,497 stars
primekg SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/primekg/SKILL.md · Queries a pinned Precision Medicine Knowledge Graph (PrimeKG) CSV for typed gene, drug, disease, and phenotype nodes…
v1.4 · audit A · 56,497 stars
primer-design SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/primer-design/SKILL.md · Designs and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target…
v1.1 · audit A · 56,497 stars
protocolsio-integration SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/protocolsio-integration/SKILL.md · Reads, validates, and safely exports protocols.io data with current official REST/MCP contracts, or creates…
v1.4 · audit A · 56,497 stars
pufferlib SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pufferlib/SKILL.md · Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training…
v1.4 · audit A · 56,497 stars
pybamm SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pybamm/SKILL.md · Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance…
v1.1 · audit A · 56,497 stars
pycalphad SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pycalphad/SKILL.md · Computes finite-temperature CALPHAD equilibria, phase fractions, and phase compositions from thermodynamic TDB…
v1.1 · audit A · 56,497 stars
pydeseq2 SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pydeseq2/SKILL.md · Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs…
v1.7 · audit A · 56,497 stars
pydicom SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pydicom/SKILL.md · Reads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data. Applies to DICOM metadata…
v1.4 · audit A · 56,497 stars
pyhealth SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pyhealth/SKILL.md · Builds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes. Use for…
v1.3 · audit A · 56,497 stars
pylabrobot SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pylabrobot/SKILL.md · Develops and reviews PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and…
v1.5 · audit A · 56,497 stars
pymatgen SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pymatgen/SKILL.md · Analyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for…
v1.5 · audit A · 56,497 stars
pymc SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pymc/SKILL.md · Builds and checks Bayesian models with PyMC, including hierarchical models, NUTS MCMC, variational inference…
v2.0 · audit A · 56,497 stars
pymoo SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pymoo/SKILL.md · Solves and validates single-, multi-, and many-objective optimization with pymoo, including NSGA-II, NSGA-III, MOEA/D…
v1.6 · audit A · 56,497 stars
pyopenms SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pyopenms/SKILL.md · Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection…
v3.0 · audit A · 56,497 stars
pysam SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pysam/SKILL.md · Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM…
v2.3 · audit A · 56,497 stars
pytdc SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pytdc/SKILL.md · Provides Therapeutics Data Commons workflows through PyTDC for registry discovery, dataset access, task-aware splits…
v1.4 · audit A · 56,497 stars
pytorch-lightning SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pytorch-lightning/SKILL.md · Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure…
v1.4 · audit A · 56,497 stars
pyzotero SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/pyzotero/SKILL.md · Manages Zotero reference libraries using the pyzotero Python client: retrieves, creates, updates, and deletes items…
v1.4 · audit A · 56,497 stars
qiime2-amplicon SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/qiime2-amplicon/SKILL.md · Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired…
v1.1 · audit A · 56,497 stars
qiskit SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/qiskit/SKILL.md · Builds, simulates, transpiles, and executes quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x…
v2.3 · audit A · 56,497 stars
qutip SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/qutip/SKILL.md · Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory…
v1.4 · audit A · 56,497 stars
rdkit SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/rdkit/SKILL.md · Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA)…
v1.5 · audit A · 56,497 stars
relion SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/relion/SKILL.md · Validates and executes RELION single-particle cryo-EM refinement and half-map postprocessing. Supports STAR…
v1.1 · audit A · 56,497 stars
relsa-severity-assessment SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/relsa-severity-assessment/SKILL.md · Supports multivariate severity assessment and exploratory endpoint-time score forecasting for laboratory animal studies…
v1.3 · audit A · 56,497 stars
research-grants SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/research-grants/SKILL.md · Supports research proposal preparation and review for NSF, NIH, DOE, DARPA, and Taiwan NSTC, including…
v1.5 · audit A · 56,497 stars
research-lookup SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/research-lookup/SKILL.md · Compiles current scholarly evidence for a scientific manuscript or research brief when the user explicitly asks to…
v1.7 · audit A · 56,497 stars
rowan SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/rowan/SKILL.md · Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and…
v1.7 · audit A · 56,497 stars
scanpy SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scanpy/SKILL.md · Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker…
v1.8 · audit A · 56,497 stars
scholar-evaluation SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scholar-evaluation/SKILL.md · Provides qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes…
v2.4 · audit A · 56,497 stars
scientific-brainstorming SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scientific-brainstorming/SKILL.md · Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit…
v1.4 · audit A · 56,497 stars
scientific-critical-thinking SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scientific-critical-thinking/SKILL.md · Evaluates scientific claims and evidence quality. Applies to experimental design validity, biases and confounders…
v1.5 · audit A · 56,497 stars
scientific-schematics SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scientific-schematics/SKILL.md · Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.7 Flash for…
v1.10 · audit A · 56,497 stars
scientific-slides SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scientific-slides/SKILL.md · Builds slide decks and presentations for research talks. Used for making PowerPoint slides, conference presentations…
v1.12 · audit A · 56,497 stars
scientific-visualization SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scientific-visualization/SKILL.md · Creates and audits truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use…
v1.4 · audit A · 56,497 stars
scientific-writing SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scientific-writing/SKILL.md · Drafts, revises, and audits scientific manuscripts or reports with explicit evidence provenance, reporting-guideline…
v2.3 · audit A · 56,497 stars
scikit-bio SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scikit-bio/SKILL.md · Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac)…
v1.4 · audit A · 56,497 stars
scikit-learn SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scikit-learn/SKILL.md · Supports machine learning in Python with scikit-learn. Applies when working with supervised learning (classification…
v1.5 · audit A · 56,497 stars
scikit-survival SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scikit-survival/SKILL.md · Builds, evaluates, and audits right-censored or competing-risk survival workflows with scikit-survival, including…
v1.4 · audit A · 56,497 stars
scvelo SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scvelo/SKILL.md · Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts. Fits deterministic or…
v2.0 · audit A · 56,497 stars
scvi-tools SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/scvi-tools/SKILL.md · Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq…
v1.4 · audit A · 56,497 stars
seaborn SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/seaborn/SKILL.md · Creates Seaborn statistical visualizations with pandas integration for distributions, relationships, categorical…
v1.5 · audit A · 56,497 stars
shap SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/shap/SKILL.md · Explain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and…
v2.3 · audit A · 56,497 stars
simpy SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/simpy/SKILL.md · Builds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy. Use for event…
v1.6 · audit A · 56,497 stars
stable-baselines3 SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/stable-baselines3/SKILL.md · Trains and evaluates single-agent reinforcement learning with Stable Baselines3 (PPO, SAC, DQN, TD3, DDPG, A2C)…
v2.0 · audit A · 56,497 stars
statistical-analysis SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/statistical-analysis/SKILL.md · Guided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis…
v2.0 · audit A · 56,497 stars
statistical-power SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/statistical-power/SKILL.md · Calculates sample sizes and statistical power for study planning. Applies when someone asks "how many…
v1.3 · audit A · 56,497 stars
statsmodels SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/statsmodels/SKILL.md · Fits and diagnoses Python statistical models including OLS, GLM, discrete and mixed models, ARIMA and SARIMAX. Supports…
v1.5 · audit A · 56,497 stars
sympy SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/sympy/SKILL.md · Performs exact symbolic mathematics with SymPy for algebra, calculus, equation solving, symbolic linear algebra…
v1.5 · audit A · 56,497 stars
tamarind SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/tamarind/SKILL.md · Provides access to a collection of open-source molecular design and structural biology tools on the Tamarind Bio…
v1.3 · audit A · 56,497 stars
tellurium SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/tellurium/SKILL.md · Simulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units…
v1.1 · audit A · 56,497 stars
tiledbvcf SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/tiledbvcf/SKILL.md · Stores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion…
v1.3 · audit A · 56,497 stars
timesfm-forecasting SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/timesfm-forecasting/SKILL.md · Performs zero-shot time-series forecasting with Google's TimesFM, including regular-grid CSV preparation, quantile…
v3.0 · audit A · 56,497 stars
torch-geometric SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/torch-geometric/SKILL.md · Supports PyTorch Geometric (PyG) graph neural networks — node/link/graph classification, message passing (GCN, GAT…
v1.4 · audit A · 56,497 stars
torchdrug SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/torchdrug/SKILL.md · Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised…
v1.4 · audit A · 56,497 stars
transformers SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/transformers/SKILL.md · Hugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning…
v1.5 · audit A · 56,497 stars
treatment-plans SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/treatment-plans/SKILL.md · Formats and structurally validates local treatment-plan documentation after clinical decisions have already been…
v2.4 · audit A · 56,497 stars
umap-learn SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/umap-learn/SKILL.md · Applies UMAP-learn to nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or…
v1.5 · audit A · 56,497 stars
uncertainty-and-units SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/uncertainty-and-units/SKILL.md · Tracks physical units and propagates measurement uncertainty in scientific calculations using pint and uncertainties…
v1.3 · audit A · 56,497 stars
usfiscaldata SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/usfiscaldata/SKILL.md · Queries the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt…
v1.5 · audit A · 56,497 stars
vaex SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/vaex/SKILL.md · Processes large tabular scientific datasets with Vaex expressions, filtered views, streamed statistics, binned…
v1.3 · audit A · 56,497 stars
venue-templates SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/venue-templates/SKILL.md · Prepares journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting…
v1.6 · audit A · 56,497 stars
waypoint-bio SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/waypoint-bio/SKILL.md · Supports work with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m…
v1.3 · audit A · 56,497 stars
what-if-oracle SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/what-if-oracle/SKILL.md · Supports structured what-if scenario analysis for research planning, experimental contingencies, and scientific project…
v1.3 · audit A · 56,497 stars
zarr-python SKILL.md skill
k-dense-ai/scientific-agent-skills · skills/zarr-python/SKILL.md · Stores and queries chunked N-D scientific arrays with Zarr-Python 3, including codecs, sharding, S3/GCS storage, and…
v1.5 · audit A · 56,497 stars
Source
github.com/k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02