README.Rmd

---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# gemma.R: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses <img src='man/figures/logo.png' align="right" height="138" />

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This is an R wrapper for [Gemma](http://gemma.msl.ubc.ca)’s RESTful [API](https://gemma.msl.ubc.ca/rest/v2/). Gemma is a web
    site, database and a set of tools for the meta-analysis, re-use and sharing 
    of genomics data, currently primarily targeted at the analysis of gene 
    expression profiles. Gemma contains data from thousands of public studies, 
    referencing thousands of published papers. 

## Installation instructions


### Bioconductor
You can install `gemma.R` through [Bioconductor](http://bioconductor.org/) with the following code:

```{r 'install', eval = FALSE}
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gemma.R")
```


## Usage

To get started with `gemma.R`, read the [vignette](https://pavlidislab.github.io/gemma.R/articles/gemma.R.html).

## Citation

To cite Gemma, please use: [Lim, N. et al., Curation of over 10 000 transcriptomic studies to enable data reuse, Database, 2021.](https://doi.org/10.1093/database/baab006)

## Code of Conduct

Please note that `gemma.R` is released with the [Bioconductor Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.