Find the best CLAUDE.md, AGENTS.md and Claude skills

garri333Skill

flowio

garri333/Skills/skills/11-scientific/flowio/SKILL.md

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.

garri333Skill

fluidsim

garri333/Skills/skills/11-scientific/fluidsim/SKILL.md

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.

garri333Reads credentialsSkill

fred-economic-data

garri333/Skills/skills/11-scientific/fred-economic-data/SKILL.md

Query FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources. Access GDP, unemployment, inflation, interest rates, exchange rates, housing, and regional data. Use for macroeconomic analysis, financial research, policy studies, economic forecasting, and academic research requiring U.S. and international economic indicators.

garri333Skill

gene-database

garri333/Skills/skills/11-scientific/gene-database/SKILL.md

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.

garri333Reads credentialsSkill

generate-image

garri333/Skills/skills/11-scientific/generate-image/SKILL.md

Generate 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.

garri333Skill

geniml

garri333/Skills/skills/11-scientific/geniml/SKILL.md

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.

garri333Skill

geo-database

garri333/Skills/skills/11-scientific/geo-database/SKILL.md

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.

garri333Skill

geopandas

garri333/Skills/skills/11-scientific/geopandas/SKILL.md

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.

garri333Skill

get-available-resources

garri333/Skills/skills/11-scientific/get-available-resources/SKILL.md

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.

Often used withusfiscaldata

garri333Skill

gget

garri333/Skills/skills/11-scientific/gget/SKILL.md

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.

garri333Skill

gtars

garri333/Skills/skills/11-scientific/gtars/SKILL.md

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.

garri333Skill

gwas-database

garri333/Skills/skills/11-scientific/gwas-database/SKILL.md

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.

Often used withuspto-database·scikit-bio·string-database

garri333Skill

histolab

garri333/Skills/skills/11-scientific/histolab/SKILL.md

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.

Often used withusfiscaldata·simpy·torch-geometric

garri333Skill

hmdb-database

garri333/Skills/skills/11-scientific/hmdb-database/SKILL.md

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

Often used withuspto-database·scikit-bio·string-database

garri333Skill

hypogenic

garri333/Skills/skills/11-scientific/hypogenic/SKILL.md

Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.

Often used withusfiscaldata·simpy·torch-geometric

garri333Skill

hypothesis-generation

garri333/Skills/skills/11-scientific/hypothesis-generation/SKILL.md

Structured 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.

garri333Skill

imaging-data-commons

garri333/Skills/skills/11-scientific/imaging-data-commons/SKILL.md

Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.

garri333Reads credentialsSkill

infographics

garri333/Skills/skills/11-scientific/infographics/SKILL.md

Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and web search for accurate data. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.

garri333Skill

iso-13485-certification

garri333/Skills/skills/11-scientific/iso-13485-certification/SKILL.md

Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.

garri333Skill

kegg-database

garri333/Skills/skills/11-scientific/kegg-database/SKILL.md

Direct 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.