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gemma.R

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

Bioconductor version: 3.23 · Package version: 3.8.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gemma.R")

Details

MaintainerPaul Pavlidis <paul@msl.ubc.ca>
AuthorJavier Castillo-Arnemann [aut] (ORCID: <https://orcid.org/0000-0002-5626-9004>), Jordan Sicherman [aut] (ORCID: <https://orcid.org/0000-0001-8160-4567>), Ogan Mancarci [aut] (ORCID: <https://orcid.org/0000-0002-1452-0889>), Guillaume Poirier-Morency [aut] (ORCID: <https://orcid.org/0000-0002-6554-0441>), Paul Pavlidis [aut, cre] (ORCID: <https://orcid.org/0000-0002-0426-5028>)
LicenseApache License (>= 2)
URLhttps://pavlidislab.github.io/gemma.R/, https://github.com/PavlidisLab/gemma.R
Bug Reportshttps://github.com/PavlidisLab/gemma.R/issues
Downloads rank432
Source branchRELEASE_3_23
biocViewsAnnotation, BatchEffect, Bayesian, DataImport, DifferentialExpression, ExperimentalDesign, GeneExpression, Microarray, Normalization, Preprocessing, SingleCell, Software, ThirdPartyClient

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packagegemma.R_3.8.0.tar.gz
Windows binary (x86_64)gemma.R_3.8.0.zip
macOS binary (arm64)gemma.R_3.8.0.tgz
macOS binary (x86_64)gemma.R_3.8.0.tgz
Dependencies

Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest, R.utils, kableExtra, base64enc

Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, listviewer, shiny