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Bioconductor - gemma.R (development version)

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

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 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) (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 See More Suggests testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, listviewer, shiny Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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