geneExpressionFromGEO: An R Package to Facilitate Data Reading from Gene Expression Omnibus (GEO)
Channel: R Consortium
Date: 2023-07-20

Davide Chicco, researcher at the University of Toronto

Gene expression profiling is a useful way to measure the activity of genes in molecular biology and, because of its effectiveness, researchers have released thousands of gene expression datasets publicly in online databases and repositories, such as Gene Expression Omnibus (GEO). To read and analyze gene expression data, the computational biology community has developed several tools and platforms, including Bioconductor, an R open-source platform of software packages that can be used to analyze these data. Despite the usefulness of Bioconductor and of its packages, it is still difficult to read gene expression data from GEO, and to assign gene symbols to the probesets of datasets. To alleviate this problem, Davide introduced a new R software package, geneExpressionFromGEO, which provides to the users the possibility to easily download gene expression data from GEO and to easily associate gene symbols to probesets. In this lightning talk, Davide described the assets of the software package, and shared the report and an example of its usage. 

PDF: https://static.sched.com/hosted_files/rmed2023a/3f/geneExpressionFromGEO%20R_Medicine%20slides%202023-06-02_2pm.pdf 

Main Sections

0:00 Introduction
0:50 Gene Expression Omnibus (GEO) and its datasets
3:30 R and GEO
5:22 geneExpressionFromGEO
10:56 Thank up!

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