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Claude Skills by aiskillstore
github.com/aiskillstore3,969 skills127 installs8,640 views
- EsmComprehensive 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 infer...Votes: 0GitHub stars: 416
- EtetoolkitPhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.Votes: 0GitHub stars: 416
- Exploratory Data AnalysisPerform 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 scien...Votes: 0GitHub stars: 416
- Fda DatabaseQuery openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.Votes: 0GitHub stars: 416
- FlowioParse 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.Votes: 0GitHub stars: 416
- Gene DatabaseQuery 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.Votes: 0GitHub stars: 416
- Generate ImageGenerate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.Votes: 0GitHub stars: 416
- GenimlThis 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.Votes: 0GitHub stars: 416
- Geo DatabaseAccess 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.Votes: 0GitHub stars: 416
- GeopandasPython 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 ...Votes: 0GitHub stars: 416
- Get Available ResourcesThis 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 runni...Votes: 0GitHub stars: 416
- GgetFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.Votes: 0GitHub stars: 416
- Gwas DatabaseQuery 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.Votes: 0GitHub stars: 416
- Hmdb DatabaseAccess Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.Votes: 0GitHub stars: 416
- Hypothesis GenerationStructured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.Votes: 0GitHub stars: 416
- Kegg DatabaseDirect REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.Votes: 0GitHub stars: 416
- Labarchive IntegrationElectronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.Votes: 0GitHub stars: 416
- LamindbThis 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, disea...Votes: 0GitHub stars: 416
- Latchbio IntegrationLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.Votes: 0GitHub stars: 416
- Latex PostersCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.Votes: 0GitHub stars: 416
- Literature ReviewConduct 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.).Votes: 0GitHub stars: 416
- MarkitdownConvert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.Votes: 0GitHub stars: 416
- MatplotlibLow-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.Votes: 0GitHub stars: 416
- MedchemMedicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.Votes: 0GitHub stars: 416
- Metabolomics Workbench DatabaseAccess 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.Votes: 0GitHub stars: 416
- ModalRun 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.Votes: 0GitHub stars: 416
- MolfeatMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.Votes: 0GitHub stars: 416
- Omero IntegrationMicroscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.Votes: 0GitHub stars: 416
- Openalex DatabaseQuery and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly works. Use for literature searches, research output analysis, citation analysis, and academic database queries.Votes: 0GitHub stars: 416
- Opentargets DatabaseQuery Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.Votes: 0GitHub stars: 416
- Opentrons IntegrationOfficial Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.Votes: 0GitHub stars: 416
- Paper 2 WebThis skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.Votes: 0GitHub stars: 416
- PathmlFull-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.Votes: 0GitHub stars: 416
- Pdb DatabaseAccess RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.Votes: 0GitHub stars: 416
- Peer ReviewStructured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.Votes: 0GitHub stars: 416
- PennylaneHardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch/JAX/TensorFlow. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.Votes: 0GitHub stars: 416
- Perplexity SearchPerform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRout...Votes: 0GitHub stars: 416
- PlotlyInteractive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures use matplotlib or scientific-visualization.Votes: 0GitHub stars: 416
- PolarsFast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.Votes: 0GitHub stars: 416
- Protocolsio IntegrationIntegration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.Votes: 0GitHub stars: 416
- Pubmed DatabaseDirect REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.Votes: 0GitHub stars: 416
- PufferlibHigh-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or standard algorithm implementations with extensive documentation, use stable-baselines3 instead.Votes: 0GitHub stars: 416
- Pydeseq2Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.Votes: 0GitHub stars: 416
- PydicomPython library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, ...Votes: 0GitHub stars: 416
- PyhealthComprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).Votes: 0GitHub stars: 416
- PylabrobotVendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.Votes: 0GitHub stars: 416
- Pymc Bayesian ModelingBayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.Votes: 0GitHub stars: 416
- PymooMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.Votes: 0GitHub stars: 416
- PyopenmsComplete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.Votes: 0GitHub stars: 416
- PytdcTherapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.Votes: 0GitHub stars: 416