gemma.R
This is thereleased version of gemma.R; for the devel version, seegemma.R.
A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
Bioconductor version: Release (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("gemma.R")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("gemma.R")For older versions of R, please refer to the appropriateBioconductor 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 | 3.6.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 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
FollowInstallation instructions to use this package in your R session.
| Source Package | gemma.R_3.6.0.tar.gz |
| Windows Binary (x86_64) | gemma.R_3.6.0.zip (64-bit only) |
| macOS Binary (x86_64) | gemma.R_3.6.0.tgz |
| macOS Binary (arm64) | gemma.R_3.6.0.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 |