cat ~/الجديد

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,...

ena-database @K-Dense-AI

Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by...

drugbank-database @K-Dense-AI

Access and analyze comprehensive drug information from the DrugBank database including drug properties,...

dnanexus-integration @K-Dense-AI

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

diffdock @K-Dense-AI

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual...

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...

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,...