Bioconductor release scheduled for October 29

gemma.R

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 (3.22)

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] ORCID iD ORCID: 0000-0002-5626-9004 , Jordan Sicherman [aut] ORCID iD ORCID: 0000-0001-8160-4567 , Ogan Mancarci [cre, aut] ORCID iD ORCID: 0000-0002-1452-0889 , Guillaume Poirier-Morency [aut] ORCID iD ORCID: 0000-0002-6554-0441

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("gemma.R")

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

Documentation

Reference Manual PDF

Details

biocViews Annotation, BatchEffect, Bayesian, DataImport, DifferentialExpression, ExperimentalDesign, GeneExpression, Microarray, Normalization, Preprocessing, SingleCell, Software, ThirdPartyClient
Version 3.5.4
In Bioconductor since BioC 3.16 (R-4.2) (3 years)
License Apache License (>= 2)
Depends
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
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, listviewer, shiny
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Package Archives

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

Source Package
Windows Binary (x86_64) gemma.R_3.5.4.zip
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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