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

Bioconductor version: Release (3.19)

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))


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 3.0.6
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
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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_3.0.6.tar.gz
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macOS Binary (x86_64) gemma.R_3.0.4.tgz
macOS Binary (arm64) gemma.R_3.0.3.tgz
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Source Repository (Developer Access) git clone
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