claude-scientific-skills-desktop

In the author's own words, from each skill's SKILL.md — showing the first 30 of 128 files.

• adaptyv

  Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for be…

  corpus/adaptyv/SKILL.md on GitHub (opens in a new tab)

• aeon

  This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series…

  corpus/aeon/SKILL.md on GitHub (opens in a new tab)

• alphafold-database

  Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

  corpus/alphafold-database/SKILL.md on GitHub (opens in a new tab)

• anndata

  This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.

  corpus/anndata/SKILL.md on GitHub (opens in a new tab)

• arboreto

  Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

  corpus/arboreto/SKILL.md on GitHub (opens in a new tab)

• astropy

  Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmologi…

  corpus/astropy/SKILL.md on GitHub (opens in a new tab)

• benchling-integration

  Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

  corpus/benchling-integration/SKILL.md on GitHub (opens in a new tab)

• biomni

  Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning wi…

  corpus/biomni/SKILL.md on GitHub (opens in a new tab)

• biopython

  Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

  corpus/biopython/SKILL.md on GitHub (opens in a new tab)

• biorxiv-database

  Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.

  corpus/biorxiv-database/SKILL.md on GitHub (opens in a new tab)

• bioservices

  Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).

  corpus/bioservices/SKILL.md on GitHub (opens in a new tab)

• brenda-database

  Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

  corpus/brenda-database/SKILL.md on GitHub (opens in a new tab)

• cellxgene-census

  Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.

  corpus/cellxgene-census/SKILL.md on GitHub (opens in a new tab)

• chembl-database

  Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

  corpus/chembl-database/SKILL.md on GitHub (opens in a new tab)

• cirq

  Quantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when working with quantum algorithms, quantum circuit design, quantum simulation (noiseless or noisy), running on quantum hardware (Google, IonQ, AQT, Pasqal), circuit optimization and compilation, noise modeling and characterization, or quantum experiments and benchmarking (VQE, QAOA,…

  corpus/cirq/SKILL.md on GitHub (opens in a new tab)

• clinicaltrials-database

  Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.

  corpus/clinicaltrials-database/SKILL.md on GitHub (opens in a new tab)

• clinpgx-database

  Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.

  corpus/clinpgx-database/SKILL.md on GitHub (opens in a new tab)

• clinvar-database

  Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.

  corpus/clinvar-database/SKILL.md on GitHub (opens in a new tab)

• cobrapy

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

  corpus/cobrapy/SKILL.md on GitHub (opens in a new tab)

• cosmic-database

  Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.

  corpus/cosmic-database/SKILL.md on GitHub (opens in a new tab)

• dask

  Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, task graphs, for larger-than-RAM datasets and parallel workflows.

  corpus/dask/SKILL.md on GitHub (opens in a new tab)

• datacommons-client

  Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity re…

  corpus/datacommons-client/SKILL.md on GitHub (opens in a new tab)

• datamol

  Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

  corpus/datamol/SKILL.md on GitHub (opens in a new tab)

• deepchem

  Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

  corpus/deepchem/SKILL.md on GitHub (opens in a new tab)

• deeptools

  NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

  corpus/deeptools/SKILL.md on GitHub (opens in a new tab)

• denario

  Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines wit…

  corpus/denario/SKILL.md on GitHub (opens in a new tab)

• diffdock

  Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

  corpus/diffdock/SKILL.md on GitHub (opens in a new tab)

• dnanexus-integration

  DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

  corpus/dnanexus-integration/SKILL.md on GitHub (opens in a new tab)

• drugbank-database

  Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or…

  corpus/drugbank-database/SKILL.md on GitHub (opens in a new tab)

• ena-database

  Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

  corpus/ena-database/SKILL.md on GitHub (opens in a new tab)

No skill matches that filter.

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