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.
labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
latchbio-integration
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
literature-review
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
markitdown
Convert various file formats (PDF, Office documents, images, audio, web content, structured data) to Markdown optimized for LLM processing. Use when converting documents to markdown, extracting text from PDFs/Office files, transcribing audio, performing OCR on images, extracting YouTube transcripts, or processing batches of files. Supports 20+ formats including DOCX, XLSX, PPTX, PDF, HTML, EPUB, CSV, JSON, images with OCR, and audio with transcription.
matchms
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
matplotlib
Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.
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.
hypothesis-generation
Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.
docx
Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.
pptx
Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.
xlsx
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
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 any task requiring detailed drug and drug target information from DrugBank.
exploratory-data-analysis
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
hypogenic
Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks.
hmdb-database
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
histolab
Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.
gwas-database
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
flowio
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
fda-database
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
christianity-aramaic-wisdom
Christian mystical wisdom through Aramaic lens - Kingdom within, Christ consciousness, feminine divine, embodiment navigation
chroma
Open-source embedding database for AI applications. Store embeddings and metadata, perform vector and full-text search, filter by metadata. Simple 4-function API. Scales from notebooks to production clusters. Use for semantic search, RAG applications, or document retrieval. Best for local development and open-source projects.
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.
chrome-devtools
Browser automation, debugging, and performance analysis using Puppeteer CLI scripts. Use for automating browsers, taking screenshots, analyzing performance, monitoring network traffic, web scraping, form automation, and JavaScript debugging.
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, QPE, randomized benchmarking).
claude-code-analyzer
Analyzes Claude Code usage patterns and provides comprehensive recommendations. Runs usage analysis, discovers GitHub community resources, suggests CLAUDE.md improvements, and fetches latest docs on-demand. Use when user wants to optimize their Claude Code workflow, create configurations (agents/skills/commands), or set up project documentation.
claude-opus-4-5-migration
Migrate prompts and code from Claude Sonnet 4.0, Sonnet 4.5, or Opus 4.1 to Opus 4.5. Use when the user wants to update their codebase, prompts, or API calls to use Opus 4.5. Handles model string updates and prompt adjustments for known Opus 4.5 behavioral differences. Does NOT migrate Haiku 4.5.
fluidsim
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
gene-database
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
generate-image
Generate or edit images using AI models (FLUX, Gemini). Use for scientific illustrations, diagrams, schematics, infographics, concept visualizations, and artistic images. Supports image editing to modify existing images (change colors, add/remove elements, style transfer). Useful for figures, posters, and visual explanations.
geniml
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
geo-database
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
geopandas
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.
get-available-resources
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
gget
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.
gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
molfeat
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
modal
Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling.
metabolomics-workbench-database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
medchem
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
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 with customizable agent orchestration.
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
deepchem
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.
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.
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 resolution, and exploring relationships between statistical entities.
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