drshailesh88/integrated_content_os

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seaborn Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted…

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vaex Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex…

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

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biomni Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecu…

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biopython Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence m…

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

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cirq Quantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when…

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clinicaltrials-database Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial det…

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

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clinvar-database Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classification…

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

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dask Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, …

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

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

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

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denario Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publi…

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

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

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

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

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fda-database Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identifi…

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

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

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

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get-available-resources This skill should be used at the start of any computationally intensive scientific task to detect and report availabl…

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

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gwas-database Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-va…

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hypogenic Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hy…

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labarchive-integration Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate wi…

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

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latchbio-integration Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serve…

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mcp-management Manage Model Context Protocol (MCP) servers - discover, analyze, and execute tools/prompts/resources from configured …

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medchem Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexit…

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modal Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running…

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molfeat Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert S…

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openalex-database Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for acad…

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pathml Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this ski…

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pdb-database Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/…

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pennylane Cross-platform Python library for quantum computing, quantum machine learning, and quantum chemistry. Enables buildin…

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polars Fast DataFrame library (Apache Arrow). Select, filter, group_by, joins, lazy evaluation, CSV/Parquet I/O, expression …

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pydeseq2 Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR co…

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pydicom Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when rea…

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pyhealth Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data…

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pymc-bayesian-modeling Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, post…

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pytdc Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molec…

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qiskit Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits. Use when working wi…

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qutip Quantum mechanics simulations and analysis using QuTiP (Quantum Toolbox in Python). Use when working with quantum sys…

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reactome-database Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interacti…

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scanpy Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes…

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scikit-learn Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression),…

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