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stanfish06

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1. ▌
   AI Sdk · stanfish06 bundle

   Vercel AI SDK expert guidance. Use when building AI-powered features — chat interfaces, text generation, structured output, tool calling, agents, MCP integration, streaming, embeddings, reranking, image generation, or working with any LLM provider.
   0 installs
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   Crewai · stanfish06

   Role-based multi-agent orchestration framework for building "Crews" of collaborating LLM agents (each with a role, goal, backstory, and optional tools) that execute sequential or hierarchical task pipelines, plus event-driven "Flows" for precise, single-LLM-call orchestration. Use when composing specialized agents (e.g. a research agent + an analysis agent + a writer agent) into a declarative pipeline for complex multi-step tasks like automated literature review or multi-agent research workflows. Distinct from LangGraph's explicit state-machine graphs and smolagents' minimal tool-calling loop — CrewAI is standalone (no LangChain dependency) and expresses orchestration as roles and delegated tasks rather than a graph or a single ReAct loop.
   0 installs
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   Depmap · stanfish06 bundle

   Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.
   0 installs
4. ▌
   Docker · stanfish06

   Containerizing and shipping applications with Docker — writing efficient Dockerfiles (multi-stage builds, layer caching, small/secure images), docker compose for multi-service local stacks, and the core build/run/debug commands. Use when creating a Dockerfile, debugging image builds, slimming images, or composing services (app + db + cache). For Claude Code dev sandboxes use devcontainer-setup; for serverless GPU runs use modal.
   0 installs
5. ▌
   Flowio · stanfish06 bundle

   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.
   0 installs
6. ▌
   Fluidsim · stanfish06 bundle

   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.
   0 installs
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   Greploop · stanfish06 bundle

   Iteratively improves a PR (GitHub), MR (GitLab), or shelved changelist (Perforce) until Greptile gives it a 5/5 confidence score with zero unresolved comments. Triggers Greptile review, fixes all actionable comments, pushes/re-shelves, re-triggers review, and repeats. Use when the user wants to fully optimize a PR/MR/CL against Greptile's code review standards.
   0 installs
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   Gwas Prs · stanfish06 bundle

   Calculate polygenic risk scores from DTC genetic data using the PGS Catalog
   0 installs
9. ▌
   Histolab · stanfish06 bundle

   Lightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images. Best for simple pipelines, dataset preparation, and quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
   0 installs
10. ▌
    Langfuse · stanfish06 bundle

    Interact with Langfuse and access its documentation: tracing, monitoring, creating datasets, running experiments, and evaluating AI applications. Use when needing to (1) query or modify Langfuse data, (2) look up Langfuse documentation, concepts, integration guides, a feature or SDK usage, or (3) do any AI engineering task (AI observability, prompt engineering/management, evaluation and evaluator management, experimentation, dataset management, evaluation-driven CI/CD, feedback collection). Invoke it for tasks in this scope even when Langfuse is not configured or explicitly mentioned.
    0 installs
11. ▌
    Logician · stanfish06 bundle

    Expert-thinking profile for Logician (proof theory / model theory / computability / set theory / formal verification (Lean, Coq, Z3)): Expert profile for logician — see AGENTS.md for field-specific methods and failure modes.
    0 installs
12. ▌
    Nextflow · stanfish06 bundle

    Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or debug a failed/-resume run. Make sure to use this skill for any reproducible scientific/bioinformatics workflow work even if the user does not say the word "Nextflow", and for authoring nf-core-compliant pipelines, modules, configs, and linting.
    0 installs
13. ▌
    Paraview · stanfish06 bundle

    ParaView scientific visualization for volume data and meshes. Use this skill when Claude needs to: (1) Visualize 3D volume data (CT, MRI, scientific simulations), (2) Create isosurfaces, slices, volume renderings, (3) Visualize vector fields with streamlines/glyphs, (4) Generate publication-quality screenshots, (5) Work with VTK, EXODUS, RAW, or other scientific data formats
    0 installs
14. ▌
    Bids · stanfish06 bundle

    Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.
    0 installs
15. ▌
    Cirq · stanfish06 bundle

    Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
    0 installs
16. ▌
    Core · stanfish06 bundle

    Core agent-browser usage guide. Read this before running any agent-browser commands. Covers the snapshot-and-ref workflow, navigating pages, interacting with elements (click, fill, type, select), extracting text and data, taking screenshots, managing tabs, handling forms and auth, waiting for content, running multiple browser sessions in parallel, and troubleshooting common failures. Use when the user asks to interact with a website, fill a form, click something, extract data, take a screenshot, log into a site, test a web app, or automate any browser task.
    0 installs
17. ▌
    Dask · stanfish06 bundle

    Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.
    0 installs
18. ▌
    Dspy · stanfish06

    DSPy declarative framework for automatic prompt optimization treating prompts as code with systematic evaluation and compilers
    0 installs
19. ▌
    Gget · stanfish06 bundle

    Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
    0 installs
20. ▌
    Htmx · stanfish06 bundle

    HTMX development guidelines for building dynamic web applications with minimal JavaScript using HTML attributes.
    0 installs
21. ▌
    Jest · stanfish06

    JavaScript testing with Jest — unit tests, mocks, spies, snapshot testing, code coverage, and configuration. Use when writing or running JavaScript/TypeScript tests, setting up a test suite with Jest, debugging failing tests, mocking modules or functions, measuring coverage, or configuring Jest in jest.config.*. Pairs with test-driven-development for the workflow/methodology. Works with React (Testing Library), Node.js, and any JS/TS project.
    0 installs
22. ▌
    Pymc · stanfish06 bundle

    Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
    0 installs
23. ▌
    Shap · stanfish06 bundle

    Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
    0 installs
24. ▌
    Protobuf · stanfish06 bundle

    Use when working with Protocol Buffer (.proto) files, buf.yaml, buf.gen.yaml, or buf.lock. Covers proto design, buf CLI, gRPC/Connect services, protovalidate constraints, schema evolution, and troubleshooting lint/breaking errors.
    0 installs
25. ▌
    Pybigwig · stanfish06

    Fast Python I/O for BigWig (continuous genome signal) and BigBed (interval annotation) files via libBigWig. Use for random-access signal queries at specific genomic coordinates (bw.values, bw.stats), computing per-region summary statistics (mean/max/coverage) over a BED file of regions, writing custom BigWig tracks from numpy arrays, and loading ChIP-seq/ATAC-seq/RNA-seq/methylation coverage tracks (e.g. produced by deeptools bamCoverage) into pandas/numpy for downstream analysis or ML feature extraction. Complements deeptools (which generates BigWig files) and chip-seq/atac-seq workflows.
    0 installs
26. ▌
    Pyhealth · stanfish06 bundle

    Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD coding, EEG events), instantiating models (Transformer, RETAIN, GAMENet, SafeDrug, MICRON, StageNet, AdaCare, CNN/RNN/MLP), training with the PyHealth Trainer, computing clinical metrics, and using medical code utilities (ICD/ATC/NDC/RxNorm lookup and cross-mapping). Use this skill whenever the user mentions PyHealth, MIMIC, eICU, OMOP, EHR modeling, clinical prediction, drug recommendation, sleep staging, medical code mapping, ICD/ATC codes, or any healthcare ML pipeline that fits the dataset → task → model → trainer → metrics pattern, even if "PyHealth" isn't named explicitly.
    0 installs
27. ▌
    Pymatgen · stanfish06 bundle

    Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
    0 installs
28. ▌
    Pyzotero · stanfish06 bundle

    Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.
    0 installs
29. ▌
    Sourmash · stanfish06

    MinHash/FracMinHash sketching for alignment-free comparison of genomes and metagenomes. Use for fast all-vs-all genome similarity and ANI estimation across thousands of genomes without alignment, taxonomic classification of metagenomes against GTDB/NCBI reference databases (sourmash gather/tax), and sequencing-cohort QC (contamination or duplicate detection). Complements upstream assembly/QC pipelines (snakemake-workflow-engine, nextflow) and feeds downstream phylogenetics; distinct from alignment-based tools like BLAST or mash-style exact-num MinHash by supporting scaled (FracMinHash) sketches that compare well across very different dataset sizes.
    0 installs
30. ▌
    Spec Kit · stanfish06 bundle

    Runs the Spec-Kit (GitHub SDD) artifact pipeline — constitution, spec, clarify, plan, tasks, analyze, implement — using its templates. Use when a feature needs a versioned spec/plan/tasks set under specs/NNN-feature/, when requirements must be pinned before any code, or when checking spec-plan-tasks consistency before implementing.
    0 installs
31. ▌
    Template · stanfish06 bundle

    Canonical rules and HTML/CSS contract for the page chrome (head boilerplate, cover, table of contents, section block, sources-section wrapper, footer, outlook-badge, design tokens) shared across Moody's Agentic Solutions HTML report skills (earnings-call-summary, peer-analysis, public-information-book, sector-analysis, etc.). Sibling of `skills/shared/citations/` using the same inlining pattern. Parent skills must read BOTH this `SKILL.md` (authoring rules: shared-layer classes, allowed per-skill overrides, outlook-badge usage) AND `assets/template.html` (canonical CSS + literal HTML snippets) before emitting any report. The asset is the source of truth for markup; this file is the source of truth for rules. Triggers on questions about the template, page chrome, cover, table of contents, footer, layout, design tokens, color palette, fonts, outlook badges, or any visual scaffolding of an HTML report skill.
    0 installs
32. ▌
    Vaex · stanfish06 bundle

    Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that do not fit in memory.
    0 installs
33. ▌
    Vite · stanfish06 bundle

    Vite build tool configuration, plugin API, SSR, and Vite 8 Rolldown migration. Use when working with Vite projects, vite.config.ts, Vite plugins, or building libraries/SSR apps with Vite.
    0 installs
34. ▌
    Gtars · stanfish06 bundle

    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.
    0 installs
35. ▌
    Modal · stanfish06 bundle

    Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accelerated workloads (training, fine-tuning, inference), serving web endpoints, scheduling batch jobs, or scaling Python code to cloud containers with the Modal SDK.
    0 installs
36. ▌
    Numba · stanfish06

    A Just-In-Time (JIT) compiler for Python that translates a subset of Python and NumPy code into fast machine code. Developed by Anaconda, Inc. Highly effective for accelerating loops, custom mathematical functions, and complex numerical algorithms. Use for @njit, @vectorize, prange, cuda.jit, numba.typed, JIT compilation, parallel loops, GPU acceleration with CUDA, Monte Carlo simulations, numerical algorithms, and high-performance Python computing.
    0 installs
37. ▌
    Pymoo · stanfish06 bundle

    Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
    0 installs
38. ▌
    Pytdc · stanfish06 bundle

    Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
    0 installs
39. ▌
    Qutip · stanfish06 bundle

    Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.
    0 installs
40. ▌
    Show Me · stanfish06 bundle

    Help the user understand the current topic visually with concise diagrams, code-shape sketches, and focused HTML artifacts.
    0 installs
41. ▌
    Ttk Viz · stanfish06

    Headless topological data analysis and visualization with the Topology ToolKit (TTK) on top of ParaView. Use this skill when Claude needs to: (1) Compute and visualize persistence diagrams, contour trees, merge trees, and Morse-Smale segmentations, (2) Extract and render critical points of scalar/vector fields, (3) Apply persistence-based topological simplification to denoise scalar fields, (4) Run TTK filters headlessly via pvpython (loading TTK plugins and using the Scalars_ naming convention).
    0 installs
42. ▌
    Arboreto · stanfish06 bundle

    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.
    0 installs
43. ▌
    Ast Grep · stanfish06 bundle

    Guide for writing ast-grep rules to perform structural code search and analysis. Use when users need to search codebases using Abstract Syntax Tree (AST) patterns, find specific code structures, or perform complex code queries that go beyond simple text search. Use when users ask to search for code patterns, find specific language constructs, or locate code with particular structural characteristics.
    0 installs
44. ▌
    Atac Seq · stanfish06 bundle

    ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.
    0 installs
45. ▌
    Botanist · stanfish06 bundle

    Expert-thinking profile for Botanist (field / herbarium / lab / computational plant science): Reasons from morphology, floras (FNA/Jepson/eFlora), voucher herbarium specimens (Darwin Core, Index Herbariorum), nomenclature (IPNI/POWO/Madrid Code), APG IV phylogeny, DNA barcoding (rbcL/matK/ITS2), community ecology (vegan adonis2/betadisper, TRY traits), and CITES/ABS ethics; treats vegetative mis-ID...
    0 installs
46. ▌
    C Review · stanfish06

    Performs comprehensive C/C++ security review for memory corruption, integer overflows, race conditions, and platform-specific vulnerabilities. Use when auditing native C/C++ applications, reviewing daemons or services for memory safety, or hunting integer overflow / use-after-free / race conditions in userspace code.
    0 installs
47. ▌
    Check Pr · stanfish06 bundle

    Checks a GitHub, GitLab, or Perforce (p4) pull request (or merge request, or shelved changelist) for unresolved review comments, failing status checks, and incomplete PR descriptions. Waits for pending checks to complete, categorizes issues as actionable or informational, and optionally fixes and resolves them. Use when the user wants to check a PR/MR/CL, address review feedback, or prepare a change for submission.
    0 installs
48. ▌
    Cns Plot · stanfish06 bundle

    Create, restyle, compose, and export compact publication-ready scientific figures with the Python cnsplots library or its source-derived Cell/Nature/Science plotting patterns. Use for cnsplots code, journal-sized Matplotlib/Seaborn figures, editable vector output, semantic scientific color systems, statistical annotations, dense rasterized layers, and mixed-size multi-panel layouts with precise text, artist, padding, margin, and panel-label control. Pair with nature-figure or scientific-visualization for broader figure strategy; use matplotlib, seaborn, adjusttext, or build-complexheatmaps when their lower-level or specialized APIs are needed.
    0 installs
49. ▌
    Cutadapt · stanfish06

    Adapter, primer, and poly-A/T trimming for high-throughput sequencing reads (FASTQ/FASTA). Use for ATAC-seq (Nextera adapter removal), ChIP-seq/CUT&RUN, small RNA-seq (preserving reads as short as ~18 nt), and amplicon/primer trimming where exact or linked adapter sequences matter more than fastp's heuristic auto-detection. Covers 3'/5'/linked adapters, IUPAC wildcards, paired-end synchronization, quality/length filtering, and demultiplexing by barcode.
    0 installs
50. ▌
    Diffdock · stanfish06 bundle

    DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.
    0 installs
51. ▌
    Evo2 Nim · stanfish06 bundle

    Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice. Use for Evo2/Evo 2, DNA generation, genomic sequence generation, hosted generation, local Docker deployment, local forward passes, layer outputs, logits, sampled probabilities, and BioNeMo NIM workflows.
    0 installs
52. ▌
    Dvc · stanfish06

    Data Version Control (DVC) for tracking large datasets/models with Git-like semantics, defining reproducible data/ML pipelines (dvc.yaml stages that only re-run when their inputs change), and lightweight experiment tracking without a server. Use when large files (VCF/BAM/FASTQ, reference genomes, model weights) can't go in Git, when you need Make/Snakemake-style selective re-execution driven by data, or when comparing many training runs locally before promoting one. Pairs with Git (code), cloud object storage (data), and Snakemake/Nextflow (compute graph).
    0 installs
53. ▌
    Ray · stanfish06

    Distributed Python compute with Ray — @ray.remote tasks/actors for cluster-scale parallelism, Ray Data for large-batch preprocessing, Ray Train for distributed model training (DDP/FSDP/DeepSpeed), Ray Tune for scalable hyperparameter search, and Ray Serve for model serving. Use when scaling a Python workload (docking screens, million-cell atlas preprocessing, hyperparameter sweeps, multi-GPU training) from a laptop to a multi-node cluster with minimal code changes. Ray Tune can use optuna as a search algorithm; Ray Train wraps pytorch-lightning-style training loops.
    0 installs
54. ▌
    Aeon · stanfish06 bundle

    Use 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 analysis with scikit-learn compatible APIs.
    0 installs
55. ▌
    Datamol · stanfish06 bundle

    Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including 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.
    0 installs
56. ▌
    Dogfood · stanfish06 bundle

    Systematically explore and test a web application to find bugs, UX issues, and other problems. Use when asked to "dogfood", "QA", "exploratory test", "find issues", "bug hunt", "test this app/site/platform", or review the quality of a web application. Produces a structured report with full reproduction evidence -- step-by-step screenshots, repro videos, and detailed repro steps for every issue -- so findings can be handed directly to the responsible teams.
    0 installs
57. ▌
    Fastapi · stanfish06

    Building HTTP/JSON APIs in Python with FastAPI — path/query/body params, Pydantic v2 models, async endpoints, dependency injection, the lifespan startup/shutdown pattern, error handling, and testing with TestClient/httpx. Use when creating a REST API or web backend in Python, adding endpoints, wiring request validation, or serving an ML model behind HTTP. Deploy with uvicorn/gunicorn (often via docker).
    0 installs
58. ▌
    Lamindb · stanfish06 bundle

    Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation with Bionty, collections, branches, storage, and workflow integrations.
    0 installs
59. ▌
    Matchms · stanfish06 bundle

    Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
    0 installs
60. ▌
    Medchem · stanfish06 bundle

    Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.
    0 installs
61. ▌
    Molfeat · stanfish06 bundle

    Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
    0 installs
62. ▌
    Opensrc · stanfish06

    Give coding agents the actual source code of any dependency. `opensrc path <pkg>` shallow-clones a package at the right version and caches it locally, printing a path you can grep/read — for npm, PyPI, crates.io, and GitHub/GitLab/Bitbucket repos. Use when you need to read a library's real implementation (not just docs) to understand internals, verify behavior, find an undocumented API, debug a dependency, or check what changed between versions. Compose with ripgrep/cat/find.
    0 installs
63. ▌
    Primekg · stanfish06 bundle

    Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
    0 installs
64. ▌
    Pydicom · stanfish06 bundle

    Python 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, radiology workflows, and healthcare imaging applications.
    0 installs
65. ▌
    Radare2 · stanfish06 bundle

    Use this skill whenever the user wants to analyze binaries with radare2/r2 from the command line, including reverse engineering, disassembly, function analysis, strings/import inspection, patching, binary diffing, hex inspection, or r2 scripting. Also use it when the user mentions PE/ELF/Mach-O/DEX/WASM files together with CLI analysis, `rabin2`, `rasm2`, `radiff2`, `r2pipe`, or asks for radare2 command help on Windows/Linux/macOS.
    0 installs
66. ▌
    Qiskit · stanfish06 bundle

    IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
    0 installs
67. ▌
    Scvelo · stanfish06 bundle

    RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.
    0 installs
68. ▌
    Seurat · stanfish06

    Single-cell RNA-seq analysis in R with Seurat v5 — QC, normalization (LogNormalize or SCTransform), dimensionality reduction, clustering, marker detection, integration of multiple samples, and interconversion with AnnData/scanpy. Use when single-cell work must stay in R/Bioconductor, when collaborators expect a Seurat object, or when following an R-based tutorial. For Python single-cell workflows use scanpy/anndata instead.
    0 installs
69. ▌
    Vitest · stanfish06

    JavaScript/TypeScript unit testing with Vitest — fast Vite-native test runner with Jest-compatible API. Use when writing or running tests in a Vite-based project (React, Vue, Svelte, vanilla TS/JS), migrating from Jest, benchmarking code, testing browser APIs with jsdom/happy-dom, or needing in-source testing. Native ES modules, TypeScript, and JSX support with zero config. Pairs with test-driven-development for the methodology.
    0 installs
70. ▌
    Xarray · stanfish06

    N-dimensional labeled arrays and datasets in Python. Built on top of NumPy and Dask. It introduces labels in the form of dimensions, coordinates, and attributes on top of raw NumPy-like arrays, making data analysis in physical sciences more intuitive and less error-prone. Use for working with multi-dimensional scientific data, NetCDF/GRIB/Zarr files, climate/weather/oceanographic datasets, remote sensing, geospatial imaging, large out-of-memory datasets with Dask, and labeled array operations.
    0 installs
71. ▌
    Zotero · stanfish06 bundle

    Use Zotero Desktop from Codex to enable/probe the local API, search a local Zotero library, list items/collections/tags, export BibTeX, insert citation keys into LaTeX or Markdown drafts, read indexed full text when requested, and import BibTeX/RIS records into Zotero through the connector server. Use when the user mentions Zotero, citations, references.bib, BibTeX export, local Zotero API, localhost:23119, or adding citations from a Zotero library.
    0 installs
72. ▌
    Adaptyv · stanfish06 bundle

    How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.
    0 installs
73. ▌
    Anndata · stanfish06 bundle

    Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
    0 installs
74. ▌
    Astropy · stanfish06 bundle

    Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.
    0 installs
75. ▌
    Atheris · stanfish06 bundle

    Sets up and runs Atheris, the coverage-guided Python fuzzer built on libFuzzer. Covers TestOneInput harnesses, FuzzedDataProvider, instrumenting both pure Python and native C extensions, and running under AddressSanitizer. Use when fuzzing a Python package, hunting memory corruption in a Python C extension, or choosing between Atheris and Hypothesis for a Python target.
    0 installs
76. ▌
    Clinpgx · stanfish06 bundle

    Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels
    0 installs
77. ▌
    Geniml · stanfish06 bundle

    Use 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.
    0 installs
78. ▌
    Gradio · stanfish06

    Building ML demos and web UIs in Python with Gradio 6 — gr.Interface for wrapping a function, gr.Blocks for custom layouts with event listeners, gr.ChatInterface for LLM chat, streaming generator outputs, gr.State, image/audio components, queueing and concurrency, launch()/share links, and mounting into FastAPI with gr.mount_gradio_app. Use when demoing a model (image, audio, text, LLM), building a quick UI around a Python function, sharing a prototype via a public link, or hosting on Hugging Face Spaces.
    0 installs
79. ▌
    Hf CLI · stanfish06 bundle

    Hugging Face Hub CLI (`hf`) for downloading, uploading, and managing repositories, models, datasets, and Spaces on the Hugging Face Hub. Replaces now deprecated `huggingface-cli` command.
    0 installs
80. ▌
    Marimo · stanfish06

    Reactive Python notebooks stored as pure .py files — cells form a dependency DAG, so changing one cell automatically reruns its dependents (or marks them stale under the lazy runtime) and hidden state cannot exist. Covers the notebook file format, marimo edit/run/export CLI, mo.ui interactive elements, SQL cells, running notebooks as apps or scripts, and sandboxed notebooks with PEP 723 inline dependencies. Use when creating or editing marimo notebooks, building interactive data apps or dashboards in pure Python, converting Jupyter notebooks, or when reproducibility/git-friendliness rules out .ipynb.
    0 installs
81. ▌
    Nextjs · stanfish06 bundle

    Next.js App Router expert guidance. Use when building, debugging, or architecting Next.js applications — routing, Server Components, Server Actions, Cache Components, layouts, middleware/proxy, data fetching, rendering strategies, and deployment on Vercel.
    0 installs
82. ▌
    Optuna · stanfish06

    Hyperparameter optimization (HPO) for ML models using Optuna. Use when tuning learning rate, regularization, architecture choices, or any numeric/categorical hyperparameter. Covers create_study/optimize quickstart, sampler selection (TPE, CMA-ES, grid, random, NSGA-II), pruners for early stopping (MedianPruner, HyperbandPruner), distributed search with RDBStorage, integrations with PyTorch Lightning and scikit-learn, and built-in visualization.
    0 installs
83. ▌
    Ot Ics · stanfish06 bundle

    Use for authorized OT/ICS security assessment covering Purdue model zoning, PLC/SCADA exposure, industrial protocol discovery, and safe passive-first evaluation.
    0 installs
84. ▌
    Pandas · stanfish06

    The workhorse library for in-memory tabular data in Python. Use for loading, cleaning, reshaping, joining, grouping, and analyzing labeled row/column data. Trigger terms include "pandas", "dataframe", "series", "csv", "parquet", "tabular data", "groupby", "pivot", "merge", "data wrangling", "data cleaning". Covers pandas 2.x and the 3.0 changes (Copy-on-Write, default string dtype, PyArrow-backed dtypes).
    0 installs
85. ▌
    Pathml · stanfish06 bundle

    Full-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.
    0 installs
86. ▌
    Plotly · stanfish06

    Use when creating interactive Python visualizations with Plotly, including pan, zoom, hover charts, dashboard figures, interactive HTML output, or 3D plots. Trigger terms include plotly, interactive chart, interactive plot, dashboard chart, hover, and plotly express. For static publication figures use matplotlib or seaborn; for visualization strategy use scientific-visualization.
    0 installs
87. ▌
    Polars · stanfish06 bundle

    High-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization, parallel execution, streaming out-of-core processing, Arrow interoperability, and optional GPU execution.
    0 installs
88. ▌
    Pytest · stanfish06

    Testing Python code with pytest — fixtures, parametrization, markers, mocking, coverage, and configuration. Use when writing or running Python tests, setting up a test suite, debugging failing tests, adding fixtures or parametrized cases, measuring coverage, or configuring pytest in pyproject.toml. Pairs with test-driven-development for the workflow/methodology.
    0 installs