geo-database
GEO Database
Overview
The Gene Expression Omnibus (GEO) is NCBI's public repository for high-throughput gene expression and functional genomics data. GEO contains over 264,000 studies with more than 8 million samples from both array-based and sequence-based experiments.
When to Use This Skill
This skill should be used when searching for gene expression datasets, retrieving experimental data, downloading raw and processed files, querying expression profiles, or integrating GEO data into computational analysis workflows.
Core Capabilities
1. Understanding GEO Data Organization
GEO organizes data hierarchically using different accession types:
Series (GSE): A complete experiment with a set of related samples
- Example: GSE123456
- Contains experimental design, samples, and overall study information
More from jimmc414/kosmos
scientific-schematics
Create publication-quality scientific diagrams, flowcharts, and schematics using Python (graphviz, matplotlib, schemdraw, networkx). Specialized in neural network architectures, system diagrams, and flowcharts. Generates SVG/EPS in figures/ folder with automated quality verification.
32pptx
Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.
18ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
17docx
Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
15scientific-slides
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
13scientific-visualization
Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.
12