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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 (3.19)

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 "4.4") 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")
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
Vignette Title HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, BatchEffect, Bayesian, DataImport, DifferentialExpression, ExperimentalDesign, GeneExpression, Microarray, Normalization, Preprocessing, SingleCell, Software, ThirdPartyClient
Version 2.1.2
In Bioconductor since BioC 3.16 (R-4.2) (1.5 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
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, digest, kableExtra
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package gemma.R_2.1.2.tar.gz
Windows Binary gemma.R_2.1.2.zip
macOS Binary (x86_64) gemma.R_2.1.2.tgz
macOS Binary (arm64) gemma.R_2.1.1.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