zwael / geosearch

GEOsearch: Extendable Search Engine for Gene Expression Omnibus

Overview

GEOsearch is an extendable search engine for NCBI GEO (Gene Expression Omnibus). Instead of directly searching the term, GEOsearch can find all the gene names contained in the search term and search all the aliases of the gene names simultaneously in GEO database. GEOsearch also provides other functions such as keyword enrichment analysis.

GEOsearch Online User Interface

GEOsearch user interface can be directly launched online without installing any software package: https://zhiji.shinyapps.io/GEOsearch. Users can also install GEOsearch on their own computers with following procedures.

GEOsearch Installation

GEOsearch software can be installed via Github. Users should have R installed on their computer before installing GEOsearch. R can be downloaded here: http://www.r-project.org/. To install the latest version of GEOsearch package via Github, run following commands in R:

if (!require("devtools"))
  install.packages("devtools")
devtools::install_github("zji90/GEOsearch")

To launch user interface after installation, run following commands in R:

library(GEOsearch)
GEOsearchui()

For users with R programming experience, command line tools are also available in GEOsearch R package. Please check the manual package included in the package for details.

Contact the Author

Author: Zhicheng Ji, Hongkai Ji

Report bugs and provide suggestions by sending email to:

Maintainer: Zhicheng Ji ([email protected])

Or open a new issue in this Github page.