Analyze publicly available RNA-seq data using NCBI GEO's GEO2R

doi.org/10.7875/togotv.2024.025
NCBI GEO (Gene Expression Omnibus) is a database of gene expression information provided and maintained by NCBI.
In this article, we will introduce how to analyze publicly available RNA-seq data using GEO2R www.ncbi.nlm.nih.gov/geo/geo2r/, a tool that enables analysis based on the data analysis environment R. The use of GEO2R has been GEO2R has been limited to microarray data, but as of March 2024, as a beta version, it can be applied to human RNA-seq data as well. (Even for human data, it may not be available for newly added data.)
0:00 Analyze publicly available RNA-seq data using NCBI GEO's GEO2R
00:09 1. About GEO2R
01:20 2. how to use GEO2R
03:01 3. checking gene expression patterns for each treatment from the table of analysis results
03:33 4. how to add columns and download analysis results
04:29 5. how to check gene expression patterns of each treatment from the table of analysis results
06:24 6. how to change detailed settings of analysis methods
07:04 7. how to check a specific gene expression profile using profile graph
07:38 8. confirming the R script used in the analysis
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