k-dense-ai/scientific-agent-skills
168 agent markdown files indexed from k-dense-ai/scientific-agent-skills. Install any of them pinned to an exact hash with mdr add k-dense-ai/scientific-agent-skills/<name>.
git:20260819.de66e10 · audit A · 46,526 stars
git:20260726.b085e11 · audit B · 46,526 stars
adaptyv skill
k-dense-ai/scientific-agent-skills · skills/adaptyv/SKILL.md · How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval…
v1.3 · audit A · 46,526 stars
aeon 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…
v1.1 · audit A · 46,526 stars
alphagenome skill
k-dense-ai/scientific-agent-skills · skills/alphagenome/SKILL.md · Look up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18…
v1.0 · audit A · 46,526 stars
analytical-method-validation skill
k-dense-ai/scientific-agent-skills · skills/analytical-method-validation/SKILL.md · Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing…
v1.1 · audit A · 46,526 stars
anndata skill
k-dense-ai/scientific-agent-skills · skills/anndata/SKILL.md · Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with…
v1.2 · audit A · 46,526 stars
arbor skill
k-dense-ai/scientific-agent-skills · skills/arbor/SKILL.md · Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective…
v1.2 · audit A · 46,526 stars
arboreto skill
k-dense-ai/scientific-agent-skills · skills/arboreto/SKILL.md · Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when…
v1.1 · audit A · 46,526 stars
astropy 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…
v1.3 · audit A · 46,526 stars
autoskill skill
k-dense-ai/scientific-agent-skills · skills/autoskill/SKILL.md · Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing…
v1.4 · audit A · 46,526 stars
benchling-integration 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…
v1.5 · audit A · 46,526 stars
bgpt-paper-search skill
k-dense-ai/scientific-agent-skills · skills/bgpt-paper-search/SKILL.md · Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP…
git:20260611.1b8fae3 · audit A · 46,526 stars
bids skill
k-dense-ai/scientific-agent-skills · skills/bids/SKILL.md · Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical…
v1.1 · audit A · 46,526 stars
biopython skill
k-dense-ai/scientific-agent-skills · skills/biopython/SKILL.md · Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB)…
v1.3 · audit A · 46,526 stars
bioservices skill
k-dense-ai/scientific-agent-skills · skills/bioservices/SKILL.md · Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL…
v1.4 · audit A · 46,526 stars
bulk-rnaseq skill
k-dense-ai/scientific-agent-skills · skills/bulk-rnaseq/SKILL.md · End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore)…
v1.1 · audit A · 46,526 stars
cellxgene-census skill
k-dense-ai/scientific-agent-skills · skills/cellxgene-census/SKILL.md · Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use…
v1.3 · audit A · 46,526 stars
cirq 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…
v1.1 · audit A · 46,526 stars
citation-management 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…
v2.1 · audit A · 46,526 stars
clinical-decision-support skill
k-dense-ai/scientific-agent-skills · skills/clinical-decision-support/SKILL.md · Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival…
v2.2 · audit A · 46,526 stars
clinical-reports skill
k-dense-ai/scientific-agent-skills · skills/clinical-reports/SKILL.md · Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety…
v2.1 · audit A · 46,526 stars
cobrapy skill
k-dense-ai/scientific-agent-skills · skills/cobrapy/SKILL.md · Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology…
v1.3 · audit A · 46,526 stars
consciousness-council skill
k-dense-ai/scientific-agent-skills · skills/consciousness-council/SKILL.md · Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill…
git:20260611.1b8fae3 · audit A · 46,526 stars
dask skill
k-dense-ai/scientific-agent-skills · skills/dask/SKILL.md · Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code…
v1.2 · audit A · 46,526 stars
database-lookup skill
k-dense-ai/scientific-agent-skills · skills/database-lookup/SKILL.md · Query documented public database APIs with explicit endpoints, filters, pagination, and provenance. Use when a…
v1.6 · audit B · 46,526 stars
datalad skill
k-dense-ai/scientific-agent-skills · skills/datalad/SKILL.md · Retrieve, version, and publish scientific datasets with DataLad and git-annex, and capture computational provenance…
v1.0 · audit A · 46,526 stars
datamol 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…
v1.2 · audit A · 46,526 stars
deepchem skill
k-dense-ai/scientific-agent-skills · skills/deepchem/SKILL.md · Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with…
v1.5 · audit A · 46,526 stars
deepspot-m skill
k-dense-ai/scientific-agent-skills · skills/deepspot-m/SKILL.md · Generate transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Use when you need…
v1.0 · audit A · 46,526 stars
deeptools 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)…
v1.3 · audit A · 46,526 stars
depmap skill
k-dense-ai/scientific-agent-skills · skills/depmap/SKILL.md · Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity…
v1.0 · audit A · 46,526 stars
dhdna-profiler skill
k-dense-ai/scientific-agent-skills · skills/dhdna-profiler/SKILL.md · Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how…
v1.1 · audit A · 46,526 stars
diffdock skill
k-dense-ai/scientific-agent-skills · skills/diffdock/SKILL.md · DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus…
v1.3 · audit A · 46,526 stars
dnanexus-integration skill
k-dense-ai/scientific-agent-skills · skills/dnanexus-integration/SKILL.md · Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows…
v2.1 · audit A · 46,526 stars
docx skill
k-dense-ai/scientific-agent-skills · skills/docx/SKILL.md · Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word…
v2.1 · audit A · 46,526 stars
esm skill
k-dense-ai/scientific-agent-skills · skills/esm/SKILL.md · Use when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or…
v1.2 · audit A · 46,526 stars
etetoolkit skill
k-dense-ai/scientific-agent-skills · skills/etetoolkit/SKILL.md · Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for…
v2.1 · audit A · 46,526 stars
exa-search skill
k-dense-ai/scientific-agent-skills · skills/exa-search/SKILL.md · Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search…
v1.2 · audit A · 46,526 stars
experimental-design skill
k-dense-ai/scientific-agent-skills · skills/experimental-design/SKILL.md · Design experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out…
v1.2 · audit A · 46,526 stars
exploratory-data-analysis skill
k-dense-ai/scientific-agent-skills · skills/exploratory-data-analysis/SKILL.md · Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON…
v1.2 · audit A · 46,526 stars
flowio skill
k-dense-ai/scientific-agent-skills · skills/flowio/SKILL.md · Read, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS…
v2.1 · audit A · 46,526 stars
fluidsim skill
k-dense-ai/scientific-agent-skills · skills/fluidsim/SKILL.md · Plan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations with explicit…
v1.2 · audit A · 46,526 stars
folklore-variant-evidence skill
k-dense-ai/scientific-agent-skills · skills/folklore-variant-evidence/SKILL.md · Retrieve ClinGen gene-disease validity assertions for a public gene or disease, and review source-linked public…
v1.0 · audit A · 46,526 stars
generate-image skill
k-dense-ai/scientific-agent-skills · skills/generate-image/SKILL.md · Generate or edit images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image…
v3.1 · audit A · 46,526 stars
geniml skill
k-dense-ai/scientific-agent-skills · skills/geniml/SKILL.md · Use Geniml for audited local genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or…
v1.2 · audit A · 46,526 stars
genomic-coordinates skill
k-dense-ai/scientific-agent-skills · skills/genomic-coordinates/SKILL.md · Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect…
v1.1 · audit A · 46,526 stars
genomic-intelligence skill
k-dense-ai/scientific-agent-skills · skills/genomic-intelligence/SKILL.md · Predict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's…
v1.2 · audit A · 46,526 stars
geomaster skill
k-dense-ai/scientific-agent-skills · skills/geomaster/SKILL.md · Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth…
v1.3 · audit A · 46,526 stars
geopandas 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…
v1.2 · audit A · 46,526 stars
get-available-resources skill
k-dense-ai/scientific-agent-skills · skills/get-available-resources/SKILL.md · Detect host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks…
v1.3 · audit A · 46,526 stars
gget skill
k-dense-ai/scientific-agent-skills · skills/gget/SKILL.md · Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence…
v1.5 · audit A · 46,526 stars
ginkgo-cloud-lab skill
k-dense-ai/scientific-agent-skills · skills/ginkgo-cloud-lab/SKILL.md · Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab…
v2.1 · audit A · 46,526 stars
glycoengineering skill
k-dense-ai/scientific-agent-skills · skills/glycoengineering/SKILL.md · Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict…
v1.2 · audit B · 46,526 stars
gtars skill
k-dense-ai/scientific-agent-skills · skills/gtars/SKILL.md · Use Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization…
v1.3 · audit A · 46,526 stars
histolab skill
k-dense-ai/scientific-agent-skills · skills/histolab/SKILL.md · Lightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction…
v1.3 · audit A · 46,526 stars
hugging-science skill
k-dense-ai/scientific-agent-skills · skills/hugging-science/SKILL.md · Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate…
v1.3 · audit A · 46,526 stars
hypogenic 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…
v1.2 · audit A · 46,526 stars
hypothesis-generation skill
k-dense-ai/scientific-agent-skills · skills/hypothesis-generation/SKILL.md · Formulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational…
v2.2 · audit A · 46,526 stars
imaging-data-commons skill
k-dense-ai/scientific-agent-skills · skills/imaging-data-commons/SKILL.md · Query and download public cancer imaging data from NCI Imaging Data Commons. Invoke for any question about IDC…
v1.5 · audit A · 46,526 stars
infographics skill
k-dense-ai/scientific-agent-skills · skills/infographics/SKILL.md · Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3.6 Flash for…
v1.7 · audit A · 46,526 stars
iso-standards-readiness 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 -…
v1.1 · audit A · 46,526 stars
lab-hardware-cad skill
k-dense-ai/scientific-agent-skills · skills/lab-hardware-cad/SKILL.md · Design custom laboratory hardware as parametric build123d models and export fabrication-ready STEP, STL, and DXF files…
v1.3 · audit A · 46,526 stars
labarchive-integration skill
k-dense-ai/scientific-agent-skills · skills/labarchive-integration/SKILL.md · Securely integrate with the official LabArchives ELN REST-like API and Inventory API v1. Use for regional endpoint…
v1.2 · audit A · 46,526 stars
lamindb skill
k-dense-ai/scientific-agent-skills · skills/lamindb/SKILL.md · Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers…
v1.2 · audit A · 46,526 stars
latchbio-integration skill
k-dense-ai/scientific-agent-skills · skills/latchbio-integration/SKILL.md · Build, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and…
v2.1 · audit A · 46,526 stars
latex-posters skill
k-dense-ai/scientific-agent-skills · skills/latex-posters/SKILL.md · Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference…
v1.7 · audit A · 46,526 stars
liteparse 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…
v1.2 · audit A · 46,526 stars
literature-review skill
k-dense-ai/scientific-agent-skills · skills/literature-review/SKILL.md · Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv…
v1.8 · audit B · 46,526 stars
markdown-mermaid-writing skill
k-dense-ai/scientific-agent-skills · skills/markdown-mermaid-writing/SKILL.md · Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis…
v1.1 · audit A · 46,526 stars
market-research-reports skill
k-dense-ai/scientific-agent-skills · skills/market-research-reports/SKILL.md · Build evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for…
v1.3 · audit A · 46,526 stars
markitdown skill
k-dense-ai/scientific-agent-skills · skills/markitdown/SKILL.md · Convert heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and…
v2.2 · audit A · 46,526 stars
matchms skill
k-dense-ai/scientific-agent-skills · skills/matchms/SKILL.md · Process, clean, compare, and search tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization…
v2.1 · audit A · 46,526 stars
matlab skill
k-dense-ai/scientific-agent-skills · skills/matlab/SKILL.md · Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data…
v1.2 · audit A · 46,526 stars
matplotlib skill
k-dense-ai/scientific-agent-skills · skills/matplotlib/SKILL.md · Low-level plotting library for full customization. Use when you need fine-grained control over every plot element…
v1.2 · audit A · 46,526 stars
medchem skill
k-dense-ai/scientific-agent-skills · skills/medchem/SKILL.md · Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert…
v1.2 · audit A · 46,526 stars
modal 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…
v1.3 · audit F · 46,526 stars
molecular-dynamics skill
k-dense-ai/scientific-agent-skills · skills/molecular-dynamics/SKILL.md · Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems…
v1.1 · audit A · 46,526 stars
molfeat skill
k-dense-ai/scientific-agent-skills · skills/molfeat/SKILL.md · Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert…
v1.2 · audit A · 46,526 stars
ncats-arax 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…
v1.0 · audit A · 46,526 stars
networkx skill
k-dense-ai/scientific-agent-skills · skills/networkx/SKILL.md · Create, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with network/graph…
v1.2 · audit A · 46,526 stars
neurokit2 skill
k-dense-ai/scientific-agent-skills · skills/neurokit2/SKILL.md · Use NeuroKit2 to build or audit reproducible research workflows for physiological time-series preprocessing…
v1.2 · audit A · 46,526 stars
neuropixels-analysis skill
k-dense-ai/scientific-agent-skills · skills/neuropixels-analysis/SKILL.md · Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB…
v2.4 · audit A · 46,526 stars
nextflow skill
k-dense-ai/scientific-agent-skills · skills/nextflow/SKILL.md · Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions…
v1.2 · audit B · 46,526 stars
omero-integration skill
k-dense-ai/scientific-agent-skills · skills/omero-integration/SKILL.md · Securely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI…
v1.4 · audit A · 46,526 stars
onekgpd skill
k-dense-ai/scientific-agent-skills · skills/onekgpd/SKILL.md · Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual…
v1.2 · audit A · 46,526 stars
ontology-term-resolution skill
k-dense-ai/scientific-agent-skills · skills/ontology-term-resolution/SKILL.md · Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup…
v1.2 · audit A · 46,526 stars
open-notebook skill
k-dense-ai/scientific-agent-skills · skills/open-notebook/SKILL.md · Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when…
v1.3 · audit A · 46,526 stars
openpiv skill
k-dense-ai/scientific-agent-skills · skills/openpiv/SKILL.md · Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs…
v1.1 · audit A · 46,526 stars
opentrons-integration skill
k-dense-ai/scientific-agent-skills · skills/opentrons-integration/SKILL.md · Author, review, migrate, simulate, and troubleshoot official Opentrons Python Protocol API v2 protocols for Flex and…
v2.1 · audit A · 46,526 stars
optimize-for-gpu 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…
v1.4 · audit A · 46,526 stars
pacsomatic skill
k-dense-ai/scientific-agent-skills · skills/pacsomatic/SKILL.md · Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user…
v1.2 · audit A · 46,526 stars
paper-lookup skill
k-dense-ai/scientific-agent-skills · skills/paper-lookup/SKILL.md · Search 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA…
v2.2 · audit A · 46,526 stars
paperclip skill
k-dense-ai/scientific-agent-skills · skills/paperclip/SKILL.md · Search and read full-text biomedical papers, FDA/PMDA/EMA regulatory documents, clinical trial registries, and…
v1.3 · audit B · 46,526 stars
paperzilla skill
k-dense-ai/scientific-agent-skills · skills/paperzilla/SKILL.md · Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent…
v1.0 · audit A · 46,526 stars
parallel-web skill
k-dense-ai/scientific-agent-skills · skills/parallel-web/SKILL.md · Use Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and…
v1.3 · audit A · 46,526 stars
pathml skill
k-dense-ai/scientific-agent-skills · skills/pathml/SKILL.md · Use PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and QC…
v1.2 · audit A · 46,526 stars
pathogen-variant-surveillance skill
k-dense-ai/scientific-agent-skills · skills/pathogen-variant-surveillance/SKILL.md · Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are…
v1.1 · audit A · 46,526 stars
pathway-enrichment skill
k-dense-ai/scientific-agent-skills · skills/pathway-enrichment/SKILL.md · Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use…
v1.1 · audit A · 46,526 stars
pdf skill
k-dense-ai/scientific-agent-skills · skills/pdf/SKILL.md · Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables…
v1.2 · audit A · 46,526 stars
peer-review skill
k-dense-ai/scientific-agent-skills · skills/peer-review/SKILL.md · Prepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized…
v2.2 · audit B · 46,526 stars
pennylane skill
k-dense-ai/scientific-agent-skills · skills/pennylane/SKILL.md · Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via…
v1.2 · audit A · 46,526 stars
phylogenetics skill
k-dense-ai/scientific-agent-skills · skills/phylogenetics/SKILL.md · Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree…
v1.2 · audit A · 46,526 stars
pi-agent skill
k-dense-ai/scientific-agent-skills · skills/pi-agent/SKILL.md · Build with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring…
v1.4 · audit A · 46,526 stars
pkpd-modeling skill
k-dense-ai/scientific-agent-skills · skills/pkpd-modeling/SKILL.md · Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population…
v1.2 · audit A · 46,526 stars
polars-bio skill
k-dense-ai/scientific-agent-skills · skills/polars-bio/SKILL.md · High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge…
v1.1 · audit A · 46,526 stars
polars skill
k-dense-ai/scientific-agent-skills · skills/polars/SKILL.md · High-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data…
v1.2 · audit A · 46,526 stars
pptx-posters skill
k-dense-ai/scientific-agent-skills · skills/pptx-posters/SKILL.md · Create and audit editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and…
v2.2 · audit A · 46,526 stars
pptx skill
k-dense-ai/scientific-agent-skills · skills/pptx/SKILL.md · Use this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes…
v2.1 · audit A · 46,526 stars
primekg skill
k-dense-ai/scientific-agent-skills · skills/primekg/SKILL.md · Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases…
v1.2 · audit A · 46,526 stars
protocolsio-integration skill
k-dense-ai/scientific-agent-skills · skills/protocolsio-integration/SKILL.md · Read, validate, and safely export protocols.io data with current official REST/MCP contracts, or create non-executing…
v1.2 · audit A · 46,526 stars
pufferlib skill
k-dense-ai/scientific-agent-skills · skills/pufferlib/SKILL.md · Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training…
v1.2 · audit A · 46,526 stars
pydeseq2 skill
k-dense-ai/scientific-agent-skills · skills/pydeseq2/SKILL.md · Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR…
v1.4 · audit A · 46,526 stars
pydicom skill
k-dense-ai/scientific-agent-skills · skills/pydicom/SKILL.md · Use pydicom to read, inspect, write, transform, and safely preflight local DICOM datasets and pixel data. Applies to…
v1.2 · audit A · 46,526 stars
pyhealth skill
k-dense-ai/scientific-agent-skills · skills/pyhealth/SKILL.md · Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV…
v1.1 · audit A · 46,526 stars
pylabrobot skill
k-dense-ai/scientific-agent-skills · skills/pylabrobot/SKILL.md · Develop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and…
v1.3 · audit A · 46,526 stars
pymatgen skill
k-dense-ai/scientific-agent-skills · skills/pymatgen/SKILL.md · Analyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs…
v1.3 · audit A · 46,526 stars
pymc skill
k-dense-ai/scientific-agent-skills · skills/pymc/SKILL.md · Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison…
v1.4 · audit A · 46,526 stars
pymoo skill
k-dense-ai/scientific-agent-skills · skills/pymoo/SKILL.md · Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT…
v1.4 · audit A · 46,526 stars
pyopenms skill
k-dense-ai/scientific-agent-skills · skills/pyopenms/SKILL.md · Complete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection…
v2.1 · audit A · 46,526 stars
pysam skill
k-dense-ai/scientific-agent-skills · skills/pysam/SKILL.md · Python/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF…
v2.1 · audit A · 46,526 stars
pytdc skill
k-dense-ai/scientific-agent-skills · skills/pytdc/SKILL.md · Use Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset access…
v1.2 · audit A · 46,526 stars
pytorch-lightning 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…
v1.2 · audit A · 46,526 stars
pyzotero skill
k-dense-ai/scientific-agent-skills · skills/pyzotero/SKILL.md · Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and…
v1.2 · audit A · 46,526 stars
qiskit skill
k-dense-ai/scientific-agent-skills · skills/qiskit/SKILL.md · Build, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x…
v2.1 · audit A · 46,526 stars
qutip 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…
v1.2 · audit A · 46,526 stars
rdkit 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)…
v1.3 · audit A · 46,526 stars
relsa-severity-assessment skill
k-dense-ai/scientific-agent-skills · skills/relsa-severity-assessment/SKILL.md · Multivariate severity assessment and humane endpoint prediction for laboratory animal studies using the RELSA (RELative…
v1.1 · audit A · 46,526 stars
research-grants skill
k-dense-ai/scientific-agent-skills · skills/research-grants/SKILL.md · Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review…
v1.3 · audit A · 46,526 stars
research-lookup skill
k-dense-ai/scientific-agent-skills · skills/research-lookup/SKILL.md · Compile current scholarly evidence for a scientific manuscript or research brief. Use when the user explicitly asks to…
v1.5 · audit A · 46,526 stars
rowan 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…
v1.5 · audit A · 46,526 stars
scanpy skill
k-dense-ai/scientific-agent-skills · skills/scanpy/SKILL.md · Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE)…
v1.6 · audit A · 46,526 stars
scholar-evaluation skill
k-dense-ai/scientific-agent-skills · skills/scholar-evaluation/SKILL.md · Provide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes…
v2.2 · audit A · 46,526 stars
scientific-brainstorming skill
k-dense-ai/scientific-agent-skills · skills/scientific-brainstorming/SKILL.md · Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit…
v1.2 · audit A · 46,526 stars
scientific-critical-thinking skill
k-dense-ai/scientific-agent-skills · skills/scientific-critical-thinking/SKILL.md · Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and…
v1.3 · audit A · 46,526 stars
scientific-schematics skill
k-dense-ai/scientific-agent-skills · skills/scientific-schematics/SKILL.md · Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.6…
v1.7 · audit A · 46,526 stars
scientific-slides skill
k-dense-ai/scientific-agent-skills · skills/scientific-slides/SKILL.md · Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference…
v1.8 · audit A · 46,526 stars
scientific-visualization skill
k-dense-ai/scientific-agent-skills · skills/scientific-visualization/SKILL.md · Create and audit truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use…
v1.2 · audit A · 46,526 stars
scientific-writing skill
k-dense-ai/scientific-agent-skills · skills/scientific-writing/SKILL.md · Draft, revise, and audit scientific manuscripts or reports with explicit evidence provenance, reporting-guideline…
v2.1 · audit A · 46,526 stars
scikit-bio 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)…
v1.2 · audit A · 46,526 stars
scikit-learn skill
k-dense-ai/scientific-agent-skills · skills/scikit-learn/SKILL.md · Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression)…
v1.3 · audit A · 46,526 stars
scikit-survival skill
k-dense-ai/scientific-agent-skills · skills/scikit-survival/SKILL.md · Build, evaluate, and audit right-censored or competing-risk survival workflows with scikit-survival, including…
v1.2 · audit A · 46,526 stars
scvelo skill
k-dense-ai/scientific-agent-skills · skills/scvelo/SKILL.md · RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer…
v1.2 · audit A · 46,526 stars
scvi-tools skill
k-dense-ai/scientific-agent-skills · skills/scvi-tools/SKILL.md · Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer…
v1.2 · audit A · 46,526 stars
seaborn skill
k-dense-ai/scientific-agent-skills · skills/seaborn/SKILL.md · Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and…
v1.3 · audit A · 46,526 stars
shap 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…
v2.1 · audit A · 46,526 stars
simpy skill
k-dense-ai/scientific-agent-skills · skills/simpy/SKILL.md · Build, inspect, test, and analyze bounded process-based discrete-event simulations with SimPy, including events…
v1.4 · audit A · 46,526 stars
stable-baselines3 skill
k-dense-ai/scientific-agent-skills · skills/stable-baselines3/SKILL.md · Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for…
v1.3 · audit A · 46,526 stars
statistical-analysis 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…
v1.2 · audit A · 46,526 stars
statistical-power skill
k-dense-ai/scientific-agent-skills · skills/statistical-power/SKILL.md · Sample-size and statistical power calculations for planning studies. Use whenever someone asks "how many…
v1.1 · audit A · 46,526 stars
statsmodels skill
k-dense-ai/scientific-agent-skills · skills/statsmodels/SKILL.md · Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with…
v1.3 · audit A · 46,526 stars
sympy skill
k-dense-ai/scientific-agent-skills · skills/sympy/SKILL.md · Use when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code…
v1.3 · audit A · 46,526 stars
tamarind skill
k-dense-ai/scientific-agent-skills · skills/tamarind/SKILL.md · Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its…
v1.1 · audit A · 46,526 stars
tiledbvcf skill
k-dense-ai/scientific-agent-skills · skills/tiledbvcf/SKILL.md · Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample…
v1.1 · audit A · 46,526 stars
timesfm-forecasting skill
k-dense-ai/scientific-agent-skills · skills/timesfm-forecasting/SKILL.md · Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales…
v1.2 · audit A · 46,526 stars
torch-geometric skill
k-dense-ai/scientific-agent-skills · skills/torch-geometric/SKILL.md · PyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT…
v1.2 · audit A · 46,526 stars
torchdrug skill
k-dense-ai/scientific-agent-skills · skills/torchdrug/SKILL.md · Build and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised…
v1.2 · audit A · 46,526 stars
transformers 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…
v1.3 · audit A · 46,526 stars
treatment-plans skill
k-dense-ai/scientific-agent-skills · skills/treatment-plans/SKILL.md · Format and structurally validate local treatment-plan documentation after clinical decisions have already been supplied…
v2.2 · audit A · 46,526 stars
umap-learn skill
k-dense-ai/scientific-agent-skills · skills/umap-learn/SKILL.md · Use UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or…
v1.3 · audit A · 46,526 stars
uncertainty-and-units skill
k-dense-ai/scientific-agent-skills · skills/uncertainty-and-units/SKILL.md · Track physical units and propagate measurement uncertainty in scientific calculations using pint and uncertainties. Use…
v1.1 · audit A · 46,526 stars
usfiscaldata skill
k-dense-ai/scientific-agent-skills · skills/usfiscaldata/SKILL.md · Query the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt…
v1.3 · audit A · 46,526 stars
vaex skill
k-dense-ai/scientific-agent-skills · skills/vaex/SKILL.md · Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex…
v1.1 · audit A · 46,526 stars
venue-templates skill
k-dense-ai/scientific-agent-skills · skills/venue-templates/SKILL.md · Prepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting…
v1.3 · audit A · 46,526 stars
waypoint-bio skill
k-dense-ai/scientific-agent-skills · skills/waypoint-bio/SKILL.md · Use when working with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m…
v1.1 · audit A · 46,526 stars
what-if-oracle skill
k-dense-ai/scientific-agent-skills · skills/what-if-oracle/SKILL.md · Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card…
v1.1 · audit A · 46,526 stars
xlsx skill
k-dense-ai/scientific-agent-skills · skills/xlsx/SKILL.md · Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary…
v2.2 · audit A · 46,526 stars
zarr-python skill
k-dense-ai/scientific-agent-skills · skills/zarr-python/SKILL.md · Chunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec…
v1.3 · audit A · 46,526 stars
Source
github.com/k-dense-ai/scientific-agent-skills · 46,526 stars · license MIT · pushed 2026-09-21