Welcome to the new bioconductor.org!


A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Bioconductor version: Release (3.18)

Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. 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.

Author: Javier Castillo-Arnemann [aut] , Jordan Sicherman [aut] , Ogan Mancarci [cre, aut] , Guillaume Poirier-Morency [aut]

Maintainer: Ogan Mancarci <ogan.mancarci at gmail.com>

Citation (from within R, enter citation("gemma.R")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

A meta analysis on effects of Parkinson's Disease using Gemma.R HTML R Script
Accessing curated gene expression data with gemma.R HTML R Script
Reference Manual PDF


biocViews Annotation, BatchEffect, Bayesian, DataImport, DifferentialExpression, ExperimentalDesign, GeneExpression, Microarray, Normalization, Preprocessing, SingleCell, Software, ThirdPartyClient
Version 2.0.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Apache License (>= 2)
Imports magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest
System Requirements
URL https://pavlidislab.github.io/gemma.R/ https://github.com/PavlidisLab/gemma.R
Bug Reports https://github.com/PavlidisLab/gemma.R/issues
See More
Suggests testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, digest
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package gemma.R_2.0.0.tar.gz
Windows Binary gemma.R_2.0.0.zip
macOS Binary (x86_64) gemma.R_2.0.0.tgz
macOS Binary (arm64) gemma.R_2.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gemma.R
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gemma.R
Bioc Package Browser https://code.bioconductor.org/browse/gemma.R/
Package Short Url https://bioconductor.org/packages/gemma.R/
Package Downloads Report Download Stats