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oimiragieo skills

Find 468 skills from 1 repo created by oimiragieo on GitHub.

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468 skills
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assistant-behavior-rules

oimiragieo/agent-studio

6
This skill helps you enforce assistant-behavior-rules by reviewing code for best practices, proposing improvements, and explaining rationale for design
astro-expert

oimiragieo/agent-studio

6
This skill helps you improve Astro apps by applying best practices for components, content, data fetching, and deployments.
latex-posters

oimiragieo/agent-studio

6
Create 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.
security-architect

oimiragieo/agent-studio

6
This skill helps you strengthen security architecture, perform threat modeling, and enforce OWASP Top 10 and secure coding practices across code and
rule-auditor

oimiragieo/agent-studio

6
This skill validates code against coding standards, identifies violations, and suggests precise fixes to improve quality and security.
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chrome-extension-expert

oimiragieo/agent-studio

6
This skill helps you build secure, well-architected Chrome extensions by reviewing code, suggesting improvements, and guiding architecture and manifest best
on-call-handoff-patterns

oimiragieo/agent-studio

6
Master on-call shift handoffs with context transfer, escalation procedures, and documentation. Use when transitioning on-call responsibilities, documenting shift summaries, or improving on-call processes.
code-style-validator

oimiragieo/agent-studio

6
This skill validates JavaScript/TypeScript code style using AST analysis to enforce naming, formatting, and import conventions with fast feedback.
text-to-sql

oimiragieo/agent-studio

6
This skill converts natural language questions into parameterized SQL using schema context, ensuring safe, optimized queries for analysis and reporting.
docker-compose

oimiragieo/agent-studio

6
This skill helps you manage multi-container applications with docker compose, enabling quick orchestration, logs, and troubleshooting for local development.
fiber-routing-and-csrf-protection

oimiragieo/agent-studio

6
This skill helps ensure fiber routing and CSRF protection compliance by enforcing middleware usage, HTMX handling, and server-side rendering templates.
insecure-defaults

oimiragieo/agent-studio

6
This skill detects insecure defaults in JavaScript applications, flagging hardcoded credentials, weak crypto, unsafe configs, and misconfigurations to guide
gwas-database

oimiragieo/agent-studio

6
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.
form-and-actions-in-sveltekit

oimiragieo/agent-studio

6
This skill helps enforce SvelteKit form actions and client-side validation with progressive enhancement, guiding server handling and refactoring for best
jupyter-notebook-best-practices

oimiragieo/agent-studio

6
This skill helps you enforce Jupyter notebook best practices by reviewing structure, documentation, and reproducibility, and suggesting concrete improvements.
qiskit

oimiragieo/agent-studio

6
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.
mobile-ui-development-rule

oimiragieo/agent-studio

6
This skill helps enforce mobile UI development best practices, optimize navigation, state management, and styling for consistent, performant apps.
gget

oimiragieo/agent-studio

6
Fast 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.
gtars

oimiragieo/agent-studio

6
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.
labarchive-integration

oimiragieo/agent-studio

6
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
matchms

oimiragieo/agent-studio

6
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.
markitdown

oimiragieo/agent-studio

6
Convert 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.
pennylane

oimiragieo/agent-studio

6
Hardware-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.
mobile-first-design-rules

oimiragieo/agent-studio

6
This skill analyzes code for mobile-first design rules, applying Tailwind responsive utilities and fluid typography to optimize for small screens.
pydeseq2

oimiragieo/agent-studio

6
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
pydicom

oimiragieo/agent-studio

6
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.
pysam

oimiragieo/agent-studio

6
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
pytdc

oimiragieo/agent-studio

6
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
reactome-database

oimiragieo/agent-studio

6
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
scikit-bio

oimiragieo/agent-studio

6
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
pipeline-reflection-ux

oimiragieo/agent-studio

6
This skill helps improve router-facing pipeline UX by making Step 0 visible, emitting completion, summarizing outcomes, and batching notifications.
planning-with-files

oimiragieo/agent-studio

6
This skill uses manuscript-style file-based planning to manage complex tasks with persistent task_plan.md, findings.md, and progress.md.
zinc-database

oimiragieo/agent-studio

6
Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
test-generator

oimiragieo/agent-studio

6
This skill generates unit, integration, API, and E2E tests from specifications and code, ensuring coverage and alignment with project patterns.
ios-expert

oimiragieo/agent-studio

6
This skill helps you improve iOS apps with SwiftUI and UIKit by enforcing best practices, architecture guidance, and thoughtful refactoring.
prd-generator

oimiragieo/agent-studio

6
This skill generates structured PRDs using a problem-first, hypothesis-driven approach with MoSCoW prioritization and implementation phases for traceable
prioritize-python-3-10-features

oimiragieo/agent-studio

6
This skill helps you prioritize Python 3.12+ features by auditing code, suggesting modern syntax, and refactoring for forward compatibility.
function-length-and-responsibility

oimiragieo/agent-studio

6
This skill helps enforce the single responsibility principle by reviewing JavaScript functions for short, focused purposes and suggesting clean refactors.
pytorch-lightning

oimiragieo/agent-studio

6
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.
react-best-practices-vercel

oimiragieo/agent-studio

6
This skill helps optimize React and Next.js performance by applying Vercel's best practices for components, pages, and data fetching.
react-expert

oimiragieo/agent-studio

6
This skill reviews React code, applies modern patterns, and helps design accessible, high-performance components with hooks and state management.
docx

oimiragieo/agent-studio

6
Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
umap-learn

oimiragieo/agent-studio

6
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
deepchem

oimiragieo/agent-studio

6
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.
sequential-thinking

oimiragieo/agent-studio

6
This skill guides structured multi-step analysis and planning by breaking problems into steps, revising plans, and verifying hypotheses.
recommend-evolution

oimiragieo/agent-studio

6
This skill detects capability gaps and records standardized evolution recommendations to guide planning across reflection, routing, and integration contexts.
research-synthesis

oimiragieo/agent-studio

6
This skill gathers and synthesizes research before artifact creation, grounding design decisions in current best practices, patterns, and risk-aware
pdf

oimiragieo/agent-studio

6
PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.
restcontroller-conventions

oimiragieo/agent-studio

6
This skill enforces restcontroller conventions for JavaScript/Java backends, ensuring proper annotations, routing, error handling, and ApiResponse usage.
ripgrep

oimiragieo/agent-studio

6
This skill provides fast code search using a custom ripgrep binary with regex, ignore patterns, and optional semantic ranking for quick discoveries.
git-expert

oimiragieo/agent-studio

6
This skill guides you through token-efficient Git workflows, translating complex operations into concise CLI commands for faster, safer version control.
histolab

oimiragieo/agent-studio

6
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
graphql-expert

oimiragieo/agent-studio

6
This skill helps you design scalable GraphQL schemas, optimize Apollo caching, and enforce best practices across client and server code.
hook-creator

oimiragieo/agent-studio

6
This skill creates and registers hooks for Claude Code, handling pre/post tool execution, memory, and session hooks to enforce safety and automation.
gitops-workflow

oimiragieo/agent-studio

6
Implement GitOps workflows with ArgoCD and Flux for automated, declarative Kubernetes deployments with continuous reconciliation. Use when implementing GitOps practices, automating Kubernetes deployments, or setting up declarative infrastructure management.
html-tailwind-css-and-javascript-expert-rule

oimiragieo/agent-studio

6
This skill helps developers write clear, readable HTML, Tailwind CSS, and JavaScript by applying current standards and best practices.
uniprot-database

oimiragieo/agent-studio

6
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
benchling-integration

oimiragieo/agent-studio

6
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.
biopython

oimiragieo/agent-studio

6
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
citation-management

oimiragieo/agent-studio

6
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
brenda-database

oimiragieo/agent-studio

6
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.
chembl-database

oimiragieo/agent-studio

6
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
dnanexus-integration

oimiragieo/agent-studio

6
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.
artifact-updater

oimiragieo/agent-studio

6
This skill updates existing artifacts across skills, agents, hooks, and more with validation, integration checks, and change management.
backend-expert

oimiragieo/agent-studio

6
This skill helps you design and review robust backend APIs and architectures with serverless patterns, performance tuning, and scalable data handling.
etetoolkit

oimiragieo/agent-studio

6
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
cellxgene-census

oimiragieo/agent-studio

6
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
pylabrobot

oimiragieo/agent-studio

6
Vendor-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.
pubchem-database

oimiragieo/agent-studio

6
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
neurokit2

oimiragieo/agent-studio

6
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
logging-module-usage

oimiragieo/agent-studio

6
This skill guides developers to apply the logging module judiciously, logging important events, warnings, and errors for clear observability.
datamol

oimiragieo/agent-studio

6
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.
memory-quality-auditor

oimiragieo/agent-studio

6
This skill analyzes memory retrieval quality, identifies drift and staleness, and generates a remediation backlog with actionable improvements.
pandas-data-manipulation-rules

oimiragieo/agent-studio

6
This skill helps you enforce pandas data manipulation best practices by reviewing code, recommending chaining, explicit loc/iloc usage, and efficient groupby
advanced-elicitation

oimiragieo/agent-studio

6
This skill enhances response quality by applying meta-cognitive reasoning with 15+ methods to reconsider and refine initial outputs.
scientific-visualization

oimiragieo/agent-studio

6
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
matplotlib

oimiragieo/agent-studio

6
Low-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.
opentrons-integration

oimiragieo/agent-studio

6
Official 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.
peer-review

oimiragieo/agent-studio

6
Structured 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.
brainstorming

oimiragieo/agent-studio

6
This skill guides collaborative design refinement from idea to structured specs, asking focused questions and presenting incremental designs for validation.
context-driven-development

oimiragieo/agent-studio

6
This skill helps teams implement context-driven development by creating and maintaining structured project context artifacts to guide AI interactions and
eval-harness-updater

oimiragieo/agent-studio

6
This skill refreshes evaluation harnesses to maintain live and fallback reliability under instability, with drift detection, timeout handling, and regression
gitflow

oimiragieo/agent-studio

6
This skill enforces gitflow best practices, guiding branch naming, merge rules, and version tagging to improve release reliability.
alpine-js-usage-rules

oimiragieo/agent-studio

6
This skill helps you enforce declarative Alpine.js usage, optimize component structure, and improve maintainability by applying best practices for x-data,
project-onboarding

oimiragieo/agent-studio

6
This skill guides you through unfamiliar codebases by discovering structure, build systems, tests, and workflows, producing persistent memories for rapid
arxiv-mcp

oimiragieo/agent-studio

6
This skill helps you discover and retrieve arXiv papers using WebFetch and Exa, delivering concise metadata and links for literature reviews.
alphafold-database

oimiragieo/agent-studio

6
Access AlphaFold 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.
anndata

oimiragieo/agent-studio

6
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.
clinvar-database

oimiragieo/agent-studio

6
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.
astropy

oimiragieo/agent-studio

6
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, cosmological distance calculations, time scale conversions, or astronomical data processing.
bioservices

oimiragieo/agent-studio

6
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
scientific-writing

oimiragieo/agent-studio

6
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
denario

oimiragieo/agent-studio

6
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.
cirq

oimiragieo/agent-studio

6
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.
clinpgx-database

oimiragieo/agent-studio

6
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
deeptools

oimiragieo/agent-studio

6
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
cosmic-database

oimiragieo/agent-studio

6
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
xlsx

oimiragieo/agent-studio

6
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
dask

oimiragieo/agent-studio

6
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.
k8s-manifest-generator

oimiragieo/agent-studio

6
Create production-ready Kubernetes manifests for Deployments, Services, ConfigMaps, and Secrets following best practices and security standards. Use when generating Kubernetes YAML manifests, creating K8s resources, or implementing production-grade Kubernetes configurations.