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This is the development version of gemma.R; for the stable release version, see gemma.R.

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

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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 guide to metadata for samples and differential expression analyses HTML R Script
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 3.1.9
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, R.utils, base64enc
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Suggests testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, kableExtra, listviewer, shiny
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Follow Installation instructions to use this package in your R session.

Source Package gemma.R_3.1.9.tar.gz
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macOS Binary (x86_64) gemma.R_3.1.9.tgz
macOS Binary (arm64) gemma.R_3.1.9.tgz
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