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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" /> <!-- badges: start --> [![R build status](https://github.com/PavlidisLab/gemma.R/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/PavlidisLab/gemma.R/actions) [![Codecov test coverage](https://codecov.io/gh/PavlidisLab/gemma.R/branch/master/graph/badge.svg)](https://codecov.io/gh/PavlidisLab/gemma.R?branch=master) [![DOI](https://img.shields.io/badge/doi-10.1093/database/baab006-yellow.svg)](https://doi.org/10.1093/database/baab006) <!-- badges: end --> 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.