AI & LLM

cosmic-database @K-Dense-AI

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

dask @K-Dense-AI

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

datacommons-client @K-Dense-AI

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

datamol @K-Dense-AI

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

deepchem @K-Dense-AI

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

deeptools @K-Dense-AI

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

denario @K-Dense-AI

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

dnanexus-integration @K-Dense-AI

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

ensembl-database @K-Dense-AI

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

esm @K-Dense-AI

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

etetoolkit @K-Dense-AI

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

exploratory-data-analysis @K-Dense-AI

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

gene-database @K-Dense-AI

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

generate-image @K-Dense-AI

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

geniml @K-Dense-AI

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

geo-database @K-Dense-AI

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

get-available-resources @K-Dense-AI

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

gget @K-Dense-AI

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

gtars @K-Dense-AI

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

histolab @K-Dense-AI

Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction,...

labarchive-integration @K-Dense-AI

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate...

lamindb @K-Dense-AI

This skill should be used when working with LaminDB, an open-source data framework for biology that makes data...

latex-posters @K-Dense-AI

Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference...

literature-review @K-Dense-AI

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv,...