Locate GEO datasets and retrieve expression data for RNA-seq and microarray studies.
npx skills add https://github.com/Hung-3008/agusta --skill geo-database-hung-3008
Please help me install this Agent Skill. Skill: geo-database Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/geo-database Command: npx skills add https://github.com/Hung-3008/agusta --skill geo-database-hung-3008
GEO hosts a vast, heterogeneous collection of gene expression datasets. This Skill provides structured guidance to locate, download, and parse GEO data (GSE/GSM/GPL) for transcriptomics analyses.
Locate a GEO accession, download its data, and begin parsing metadata for downstream analysis.
High-intent search queries and answers about installing and using this skill.
Download GEO series matrix files by locating the specific GSE accession and retrieving expression data via GEOparse, NCBI E-utilities, or FTP. This Skill guides downloading series matrices, MINiML, and SOFT files for RNA-seq and microarray transcriptomics workflows.
Batch processing across multiple GEO datasets is supported for meta-analysis workflows. You can search GEO DataSets and Groups for experiments of interest, then retrieve and parse metadata from multiple GSE/GSM records to prepare downstream gene expression analyses.
Parsing GPL platform annotations from GEO data involves retrieving MINiML or SOFT files and extracting platform metadata for downstream analysis. This Skill supports programmatic access via GEOparse and NCBI E-utilities to handle platform annotation considerations in transcriptomics studies.
GEOparse supports programmatic access to RNA-seq datasets with rate-limiting notes to manage request frequency. When retrieving GEO expression data via GEOparse, E-utilities, or FTP, rate-limiting considerations are provided to ensure stable dataset downloads.
Search NCBI E-utilities for GEO GSE accession numbers by querying GEO DataSets and Groups for experiments of interest. This Skill locates specific GSE/GSM/GPL records and retrieves corresponding series matrices, MINiML, and SOFT files for gene expression research workflows.
Victory-HugoRetrieve and parse GEO datasets using GEOparse and Biopython.
HolobiomicsLabLocate and retrieve GEO datasets and metadata for gene expression studies.
ovachieverSearch GEO datasets and download gene expression data via E-utilities and GEOparse.
nahisahoSearch ArrayExpress and BioStudies for expression experiments and retrieve metadata.
