Search, download, and parse GEO microarray and RNA-seq datasets.
npx skills add https://github.com/yf8578/clawomics --skill geo-database-yf8578
Please help me install this Agent Skill. Skill: geo-database Source: https://github.com/yf8578/clawomics/tree/main/skills/geo-database Command: npx skills add https://github.com/yf8578/clawomics --skill geo-database-yf8578
This Skill provides programmatic access to the NCBI Gene Expression Omnibus (GEO) database, enabling users to find, download, and analyze gene expression and genomics datasets.
Use the geo-database skill to search for human breast cancer RNA-seq datasets submitted in 2023.
High-intent search queries and answers about installing and using this skill.
To download and parse gene expression datasets from NCBI GEO, this Skill provides programmatic access to search and retrieve GSE, GSM, and GPL series. It uses GEOparse and Biopython to parse SOFT/MINiML files into expression matrices for transcriptomics analysis.
The best way to search for RNA-seq datasets in the GEO database is by applying specific search criteria like organism and disease. This Skill enables querying NCBI GEO to find and retrieve relevant microarray and RNA-seq datasets matching your research parameters.
Yes, you can use GEOparse and Biopython for differential expression analysis. This Skill integrates these libraries with pandas, scipy, and statsmodels to perform quality control, differential expression analysis, and clustering on retrieved gene expression data.
Yes, this approach supports both microarray and RNA-seq data retrieval from GEO. It facilitates the programmatic downloading and parsing of GSE, GSM, and GPL series datasets for comprehensive gene expression and transcriptomics analysis.
To extract expression matrices from SOFT files for meta-analysis, this Skill parses downloaded NCBI GEO data using GEOparse. It structures the genomics data using pandas and numpy, enabling downstream quality control and identification of dysregulated genes.
felixboehmSearch and download NCBI GEO datasets using Biopython and GEOparse.
MubasherMohammedAutomate differential expression analysis of proteomics data with Python libraries.
wsxwj123Search, retrieve, and integrate GEO gene expression datasets across studies.
jimmc414Search and download NCBI GEO datasets in SOFT or Matrix formats.
