gemma.R

DOI: 10.18129/B9.bioc.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 (3.17)

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>

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

Installation

To install this package, start R (version "4.3") 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

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 1.1.0
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_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64) gemma.R_1.1.0.tgz
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
Package Short Url https://bioconductor.org/packages/gemma.R/
Package Downloads Report Download Stats

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