Skills

github.com/K-Dense-AI/scientific-agent-skills55.7k

scientific-agent-skills

Turn any AI agent into an AI Scientist.

npx skills add K-Dense-AI/scientific-agent-skills -g -y
40 skills

13C Metabolic Flux

Estimates metabolic fluxes from carbon-13 isotope tracing data with fitting and diagnostics.

K-Dense-AI/scientific-agent-skills55.7k

Adaptyv Protein Experiments

Designs protein assay experiments and submits sequences to the Adaptyv Bio Foundry API.

K-Dense-AI/scientific-agent-skills55.7k

Time Series Machine Learning

Handles time series classification, forecasting, anomaly detection and similarity search.

K-Dense-AI/scientific-agent-skills55.7k

Alphagenome

Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant...

K-Dense-AI/scientific-agent-skills55.7k

Analytical Method Validation

Plans, executes, and documents validation, verification, and transfer of analytical...

K-Dense-AI/scientific-agent-skills55.7k

Anndata

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and...

K-Dense-AI/scientific-agent-skills55.7k

Arbor

Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable...

K-Dense-AI/scientific-agent-skills55.7k

Arboreto

Infers candidate gene regulatory networks from bulk or single-cell expression data...

K-Dense-AI/scientific-agent-skills55.7k

Astropy

Core Python library for astronomy and astrophysics workflows that need Astropy APIs...

K-Dense-AI/scientific-agent-skills55.7k

Autoskill

Analyzes user-requested Screenpipe history windows to detect repeated research...

K-Dense-AI/scientific-agent-skills55.7k

Benchling Integration

Benchling Python SDK and REST API integration for registry entities, inventory, ELN...

K-Dense-AI/scientific-agent-skills55.7k

Bgpt Paper Search

Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence...

K-Dense-AI/scientific-agent-skills55.7k

Bids

Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets.

K-Dense-AI/scientific-agent-skills55.7k

Biopython

Provides Biopython workflows for sequence manipulation, file parsing...

K-Dense-AI/scientific-agent-skills55.7k

Bioservices

Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL...

K-Dense-AI/scientific-agent-skills55.7k

Bulk Rnaseq

Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level...

K-Dense-AI/scientific-agent-skills55.7k

Cantera

Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism...

K-Dense-AI/scientific-agent-skills55.7k

Cellprofiler

Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell...

K-Dense-AI/scientific-agent-skills55.7k

Cellxgene Census

Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and...

K-Dense-AI/scientific-agent-skills55.7k

Cirq

Google quantum computing framework.

K-Dense-AI/scientific-agent-skills55.7k

Citation Management

Comprehensive citation management for academic research.

K-Dense-AI/scientific-agent-skills55.7k

Clinical Decision Support

Prepares and validates research-only clinical decision-support evaluation...

K-Dense-AI/scientific-agent-skills55.7k

Clinical Reports

Creates safety-bounded draft structures and runs local deterministic checks for...

K-Dense-AI/scientific-agent-skills55.7k

Cobrapy

Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA...

K-Dense-AI/scientific-agent-skills55.7k

Consciousness Council

Structures a multi-perspective council exercise for decisions, research trade-offs, and...

K-Dense-AI/scientific-agent-skills55.7k

Dask

Scales pandas, NumPy, and custom Python research workflows beyond memory or across...

K-Dense-AI/scientific-agent-skills55.7k

Database Lookup

Queries documented public database APIs with explicit endpoints, filters, pagination...

K-Dense-AI/scientific-agent-skills55.7k

Datalad

Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and...

K-Dense-AI/scientific-agent-skills55.7k

Datamol

Pythonic wrapper around RDKit with simplified interface and sensible defaults.

K-Dense-AI/scientific-agent-skills55.7k

Deepchem

Builds molecular property prediction and MoleculeNet workflows with DeepChem, including...

K-Dense-AI/scientific-agent-skills55.7k

Deepspot M

Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with...

K-Dense-AI/scientific-agent-skills55.7k

Deeptools

NGS analysis toolkit.

K-Dense-AI/scientific-agent-skills55.7k

Depmap

Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR...

K-Dense-AI/scientific-agent-skills55.7k

Dhdna Profiler

Applies the DHDNA framework as an exploratory rubric for reasoning and writing patterns...

K-Dense-AI/scientific-agent-skills55.7k

Diffdock

Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or...

K-Dense-AI/scientific-agent-skills55.7k

Dnanexus Integration

Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy...

K-Dense-AI/scientific-agent-skills55.7k

Esm

Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and...

K-Dense-AI/scientific-agent-skills55.7k

Etetoolkit

Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other...

K-Dense-AI/scientific-agent-skills55.7k

Exa Search

Searches scientific and technical web content with Exa and extracts page or PDF text...

K-Dense-AI/scientific-agent-skills55.7k

Experimental Design

Designs experiments and studies BEFORE data is collected, choosing a design...

K-Dense-AI/scientific-agent-skills55.7k