Can this skill download raw sequencing files?

Yes, it provides methods to download supplementary files and can be configured to retrieve metadata and links for SRA (Sequence Read Archive) data.

Do I need an API key to use this skill?

While not strictly required for minor queries, it uses NCBI Entrez, which requires an email address to identify your requests to their E-utilities API.

Can I filter data by specific organisms or experimental types?

Yes, you can refine your searches using MeSH terms, organisms (e.g., Homo sapiens), study types (e.g., RNA-seq), and publication dates.

What accession types does this skill support?

It supports all major GEO accession types, including Series (GSE), Samples (GSM), Platforms (GPL), and curated DataSets (GDS).

Which Python libraries are required for this skill?

The skill primarily utilizes Biopython (Bio.Entrez) for searching and GEOparse for high-level data retrieval and parsing into Pandas DataFrames.

NCBI GEO Database Tool

Name: NCBI GEO Database Tool
Author: ricable

byricable

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Data Science & ML

Accesses and retrieves gene expression and functional genomics data from the NCBI Gene Expression Omnibus (GEO) repository.

About

This skill provides a specialized interface for interacting with the NCBI Gene Expression Omnibus (GEO), the world's largest public repository for high-throughput genomics data. It enables researchers and bioinformaticians to programmatically search for datasets (GSE), samples (GSM), and platforms (GPL), download SOFT or Matrix files, and integrate transcriptomics data directly into computational workflows. By leveraging Python libraries like GEOparse and Biopython, it simplifies the process of querying expression profiles and preparing large-scale biological data for downstream analysis.

Key Features

1 GitHub stars
Extract and pivot expression matrices for seamless transcriptomics analysis
Programmatically download and parse GSE Series and GSM Sample metadata
Search GEO DataSets and Profiles using complex keyword, organism, and condition queries
Support for multiple data formats including SOFT, Series Matrix, and Miniml
Access supplementary files and raw data via FTP and NCBI E-utilities

Use Cases

Automating the retrieval of RNA-seq or microarray datasets for comparative meta-analysis
Building automated bioinformatics pipelines that integrate public genomics data into local environments
Querying specific gene expression patterns across thousands of public biological studies

About

Key Features

1 GitHub stars
Extract and pivot expression matrices for seamless transcriptomics analysis
Programmatically download and parse GSE Series and GSM Sample metadata
Search GEO DataSets and Profiles using complex keyword, organism, and condition queries
Support for multiple data formats including SOFT, Series Matrix, and Miniml
Access supplementary files and raw data via FTP and NCBI E-utilities

Use Cases

Automating the retrieval of RNA-seq or microarray datasets for comparative meta-analysis
Building automated bioinformatics pipelines that integrate public genomics data into local environments
Querying specific gene expression patterns across thousands of public biological studies