GEOsearch v1.0.0

by Zhicheng Ji

GEOsearch

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 alias of the gene names simultaneously in GEO database. GEOsearch also provides other functions such as summarizing common biology keywords in the search results.

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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 alias of the gene names simultaneously in GEO database. GEOsearch also provides other functions such as summarizing common biology keywords in the search results.

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 GSCA. R can be downloaded here: http://www.r-project.org/. To install the latest version of GSCA package via Github, run following commands in R: ```{r } if (!require("devtools")) install.packages("devtools") devtools::install_github("GEOsearch","zji90")

To launch user interface after installation, run following commands in R:
```{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 (zji4@jhu.edu)

Or open a new issue in this Github page

Functions in GEOsearch

Name Description
GEOSearchUI GEOSearchUI
database List of species database
GEOSearchTerm GEOSearchTerm
KeyWordFreq KeyWordFreq
SampleDetail SampleDetail
term List of common biology keywords
TermAlias TermAlias
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