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 (3.24)
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 [aut]
, Guillaume Poirier-Morency [aut]
, Paul Pavlidis [aut, cre]
Maintainer: Paul Pavlidis <paul at msl.ubc.ca>
citation("gemma.R")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, BatchEffect, Bayesian, DataImport, DifferentialExpression, ExperimentalDesign, GeneExpression, Microarray, Normalization, Preprocessing, SingleCell, Software, ThirdPartyClient |
| Version | 3.9.1 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | Apache License (>= 2) |
| Depends | R (>= 4.1.0) |
| 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, pheatmap |
| 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, 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.
| Source Package | gemma.R_3.9.1.tar.gz |
| Windows Binary (x86_64) | gemma.R_3.9.1.zip |
| macOS Binary (big-sur-x86_64) | gemma.R_3.9.1.tgz |
| macOS Binary (sonoma-arm64) | gemma.R_3.9.1.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 |