gemma.R

DOI: 10.18129/B9.bioc.gemma.R  

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

Bioconductor version: Release (3.16)

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 gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Accessing curated gene expression data with gemma.R
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, BatchEffect, Bayesian, DataImport, DifferentialExpression, ExperimentalDesign, GeneExpression, Microarray, Normalization, Preprocessing, SingleCell, Software, ThirdPartyClient
Version	1.0.1
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	Apache License (>= 2)
Depends
Imports	magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64
LinkingTo
Suggests	testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis
SystemRequirements
Enhances
URL	https://pavlidislab.github.io/gemma.R/ https://github.com/PavlidisLab/gemma.R
BugReports	https://github.com/PavlidisLab/gemma.R/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	gemma.R_1.0.1.tar.gz
Windows Binary	gemma.R_1.0.1.zip
macOS Binary (x86_64)	gemma.R_1.0.1.tgz
macOS Binary (arm64)	gemma.R_1.0.1.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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive