gemma.R

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see gemma.R.

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

Bioconductor version: 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] 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 "4.4") and enter:


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

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

Documentation

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

browseVignettes("gemma.R")

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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, BatchEffect, Bayesian, DataImport, DifferentialExpression, ExperimentalDesign, GeneExpression, Microarray, Normalization, Preprocessing, SingleCell, Software, ThirdPartyClient

Version 3.2.1

In Bioconductor since BioC 3.16 (R-4.2) (2.5 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

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 gemma.R_3.2.1.tar.gz

Windows Binary (x86_64) gemma.R_3.2.1.zip

macOS Binary (x86_64) gemma.R_3.2.1.tgz

macOS Binary (arm64) gemma.R_3.2.1.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/

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Old Source Packages for BioC 3.20 Source Archive