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https://github.com/seandavi/geoquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
https://github.com/seandavi/geoquery

bioconductor bioinformatics data-science genomics ncbi-geo r rstats

Last synced: 3 days ago
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The bridge between the NCBI Gene Expression Omnibus and Bioconductor

Host: GitHub
URL: https://github.com/seandavi/geoquery
Owner: seandavi
License: mit
Created: 2013-07-19T06:44:10.000Z (over 11 years ago)
Default Branch: main
Last Pushed: 2023-11-21T21:50:32.000Z (about 1 year ago)
Last Synced: 2024-05-15T17:31:48.940Z (8 months ago)
Topics: bioconductor, bioinformatics, data-science, genomics, ncbi-geo, r, rstats
Language: R
Homepage: http://seandavi.github.io/GEOquery
Size: 19.1 MB
Stars: 82
Watchers: 6
Forks: 34
Open Issues: 18
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        ## Status

[![R-CMD-check](https://github.com/seandavi/GEOquery/workflows/R-CMD-check/badge.svg)](https://github.com/seandavi/GEOquery/actions)

[![Downloads](https://bioconductor.org/shields/downloads/release/GEOquery.svg)](https://bioconductor.org/packages/GEOquery)

[![Years in Bioc](https://bioconductor.org/shields/years-in-bioc/GEOquery.svg)](https://bioconductor.org/packages/GEOquery)

[![R-CMD-check](https://github.com/seandavi/GEOquery/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/seandavi/GEOquery/actions/workflows/R-CMD-check.yaml)

## Installation

To install from Bioconductor, use the following code:

```

# if needed, install BiocManager

install.packages("BiocManager")

# install GEOquery

BiocManager::install("GEOquery")

```

To install directly from github:

```

BiocManager::install('seandavi/GEOquery')

```

## Usage

See the full vignette in [rmarkdown](https://github.com/seandavi/GEOquery/blob/master/vignettes/GEOquery.Rmd) or visit Bioconductor for details:

- [Release version](http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html)

- [Devel version](http://www.bioconductor.org/packages/devel/bioc/html/GEOquery.html)

## How to contribute

Contributions to GEOquery development can be submitted as a [pull request](https://github.com/seandavi/GEOquery/pulls) or a [feature request issue](https://github.com/seandavi/GEOquery/issues). We recommend following the [Bioconductor coding standards](https://contributions.bioconductor.org/r-code.html) where possible.