cat ~/Nuevo

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...

clinpgx-database @K-Dense-AI

Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele...

clinicaltrials-database @K-Dense-AI

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

clinical-reports @K-Dense-AI

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports...

clinical-decision-support @K-Dense-AI

Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings,...

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,...

chembl-database @K-Dense-AI

Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve...

cellxgene-census @K-Dense-AI

Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues,...

brenda-database @K-Dense-AI

Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism...

bioservices @K-Dense-AI

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG,...

biorxiv-database @K-Dense-AI

Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences...

biopython @K-Dense-AI

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB),...

benchling-integration @K-Dense-AI

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API,...

astropy @K-Dense-AI

Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with...

arboreto @K-Dense-AI

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use...

anndata @K-Dense-AI

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with...