AI & LLM

gtars @K-Dense-AI

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic...

gget @K-Dense-AI

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold...

get-available-resources @K-Dense-AI

This skill should be used at the start of any computationally intensive scientific task to detect and report...

geo-database @K-Dense-AI

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL),...

geniml @K-Dense-AI

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for...

generate-image @K-Dense-AI

Generate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos,...

gene-database @K-Dense-AI

Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations,...

exploratory-data-analysis @K-Dense-AI

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should...

etetoolkit @K-Dense-AI

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy,...

esm @K-Dense-AI

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across...

ensembl-database @K-Dense-AI

Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis,...

dnanexus-integration @K-Dense-AI

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows,...

denario @K-Dense-AI

Multiagent AI system for scientific research assistance that automates research workflows from data analysis to...

deeptools @K-Dense-AI

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks),...

deepchem @K-Dense-AI

Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with...

datamol @K-Dense-AI

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery...

datacommons-client @K-Dense-AI

Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use...

dask @K-Dense-AI

Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy...

cosmic-database @K-Dense-AI

Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene...

cobrapy @K-Dense-AI

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems...

clinvar-database @K-Dense-AI

Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity...

clinicaltrials-database @K-Dense-AI

Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial...

citation-management @K-Dense-AI

Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract...

cirq @K-Dense-AI

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits,...