Directory / Scientific Agent Skills (K-Dense)

Scientific Agent Skills by K-Dense

177 entries from K-Dense-AI/scientific-agent-skills (52,795 GitHub stars), maintained by K-Dense Inc.. Works with: Any Agent Skills host (Claude Code, Codex, Cursor, Gemini CLI, Copilot…). Synced at commit 593377b (2026-10-19).

Science and research skills (biology, chemistry, medicine, physics, data analysis). Also installable as one collection with `npx skills add K-Dense-AI/scientific-agent-skills`.

Install a single skill with gh skill install K-Dense-AI/scientific-agent-skills SKILL (GitHub CLI 2.90+, add --agent claude-code, codex, cursor or gemini for other hosts).

177 of 177 shown. Click a column header to sort.


13c-metabolic-flux Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation,…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
adaptyv Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory p…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
aeon This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, seg…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
alphagenome Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus r…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
analytical-method-validation Plans, executes, and documents validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
anndata Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format skill—fo…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
arbor Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis a…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
arboreto Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
astropy Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time s…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
autoskill Analyzes user-requested Screenpipe history windows to detect repeated research workflows, match existing scientific skills, and stage new skill drafts…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
benchling-integration Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Us…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
bgpt-paper-search Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported statistic…	K-Dense science	skill	Science, research & learning	52,795	–	BGPT	MIT
bids Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets. Supports organizing neuroscience and biomedical data (MRI, E…	K-Dense science	skill	Science, research & learning	52,795	–	Yaroslav Halchenko	https://creativecommons.org/licenses/by/4.0/
biopython Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entr…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	Biopython License Agreement
bioservices Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protei…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	GPLv3
bulk-rnaseq Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantif…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cantera Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use …	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cellprofiler Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/ch…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cellxgene-census Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cirq Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	Apache-2.0
citation-management Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate c…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
clinical-decision-support Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governanc…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
clinical-reports Creates safety-bounded draft structures and runs local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research repor…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cobrapy Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	GPL-2.0
consciousness-council Structures a multi-perspective council exercise for decisions, research trade-offs, and creative challenges. Simulates thinking archetypes, separates …	K-Dense science	skill	Science, research & learning	52,795	–	AHK Strategies (ashrafkahoush-ux)	MIT
dask Scales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask. Covers DataFrames, Arrays, Bags, Futures, chunk…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
database-lookup Queries documented public database APIs with explicit endpoints, filters, pagination, and provenance. Used when a scientific, regulatory, financial, o…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
datalad Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and …	K-Dense science	skill	Science, research & learning	52,795	–	Dylan Pulver	MIT
datamol Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standar…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	Apache-2.0
deepchem Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked lab…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
deepspot-m Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted log1p-CPM expression from 224x224 …	K-Dense science	skill	Science, research & learning	52,795	–	Ratschlab, ETH Zurich	PolyForm-Noncommercial-1.0.0
deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq v…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD
depmap Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics biomarkers,…	K-Dense science	skill	Science, research & learning	52,795	–	Kuan-lin Huang	CC-BY-4.0
dhdna-profiler Applies the DHDNA framework as an exploratory rubric for reasoning and writing patterns in supplied text. Used for explicit requests for DHDNA, cognit…	K-Dense science	skill	Science, research & learning	52,795	–	AHK Strategies (ashrafkahoush-ux)	MIT
diffdock Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triag…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
dnanexus-integration Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Suppo…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
esm Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and Biohu…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
etetoolkit Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topolo…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	GPL-3.0-or-later
exa-search Searches scientific and technical web content with Exa and extracts page or PDF text from URLs in batches. Supports scholarly discovery with the publi…	K-Dense science	skill	Science, research & learning	52,795	–	Exa	MIT
experimental-design Designs experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results …	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
exploratory-data-analysis Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, …	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
fictiv Operates Fictiv (app.fictiv.com), the on-demand manufacturing platform, end to end in the user's browser. Covers uploading CAD parts, configuring proc…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
flowio Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, …	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
flowkit Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strat…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
fluidsim Plans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
folklore-variant-evidence Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one supp…	K-Dense science	skill	Science, research & learning	52,795	–	Helena Bioinformatics	MIT
generate-image Generates or edits images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos, illustrat…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
geniml Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenize…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
genomic-coordinates Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mism…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
genomic-intelligence Predicts regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language m…	K-Dense science	skill	Science, research & learning	52,795	–	Genomic Intelligence	MIT
geomaster Supports geospatial research workflows for remote sensing, vector and raster GIS, spatial statistics, terrain and network analysis, and machine learni…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
geopandas Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
get-available-resources Detects host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or b…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
gget Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF structur…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-2-Clause
ginkgo-cloud-lab Guides protocol selection, input preparation, pricing checks, and browser ordering on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio). Applies to cell-fr…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
glycoengineering Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan evide…	K-Dense science	skill	Science, research & learning	52,795	–	Kuan-lin Huang	Unknown
gtars Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and …	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
histolab Extracts and preprocesses whole-slide histology image tiles with Histolab. Use for WSI inspection, tissue masks, random/grid/score-based tile extracti…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	Apache-2.0
hugging-science Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. Used when selecting scientific…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
hypogenic Plans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text datasets. Use for the `hypogenic` pac…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT

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