GEO analysis with Shiny

GEO Analysis with Shiny

Summary: Developing a web tool using Shiny to analyze gene expression data from the Gene Expression Omnibus (GEO).

Description: The Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) is a public repository of gene expression data. Although GEO has its own tool, called GEO2R, for simple data analysis, statistical and bioinformatics expertise is required for more comprehensive analyses. For example, it is not straightforward to determine whether a single gene is differentially expressed across two groups. This project will involve the development of a web tool, using the R web framework Shiny, to provide users with an interface for analyzing GEO datasets.

Related work: From within R, users can download GEO datasets and extract relevant information using the 'GEOquery' library (http://bioconductor.org/packages/release/bioc/html/GEOquery.html) in order to analyze GEO datasets. The proposed project would implement this within a Shiny framework, providing users access to GEO without requiring knowledge of R.

Potential tasks (to be implemented within a web interface using Shiny):

• Download a GEO series selected by the user, extract gene expression and phenotypic information
• Pull out the gene expression values for a desired gene
• Assign individuals to two (or more) groups to determine whether the gene is differentially expressed
• Visualize expression using boxplots
• Implement additional statistical analyses

Skills required: literate programming experiences, so decent R experience is needed. Knowledge of Shiny and/or gene expression data is not required, but is recommended.

Test: Fork the package on GH and create a pull-request implementing a method for tables::tabular. Quick and dirty solution:

Mentor: Garrett Dancik ([@](mailto:dancikg {at} easternct {dot} edu)) and [Yuanbin Ru] ([@](mailto:ruyuanbin {at} gmail {dot} com))