---
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 (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
# The following initializes usage of Bioc devel
# it won't be necessary with the next version
# of Bioconductor
BiocManager::install(version='devel')
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.
