gemma.R
A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
Bioconductor version: 3.23 · Package version: 3.8.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("gemma.R")Details
| Maintainer | Paul Pavlidis <paul@msl.ubc.ca> |
| Author | Javier Castillo-Arnemann [aut] (ORCID: <https://orcid.org/0000-0002-5626-9004>), Jordan Sicherman [aut] (ORCID: <https://orcid.org/0000-0001-8160-4567>), Ogan Mancarci [aut] (ORCID: <https://orcid.org/0000-0002-1452-0889>), Guillaume Poirier-Morency [aut] (ORCID: <https://orcid.org/0000-0002-6554-0441>), Paul Pavlidis [aut, cre] (ORCID: <https://orcid.org/0000-0002-0426-5028>) |
| License | Apache License (>= 2) |
| URL | https://pavlidislab.github.io/gemma.R/, https://github.com/PavlidisLab/gemma.R |
| Bug Reports | https://github.com/PavlidisLab/gemma.R/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, BatchEffect, Bayesian, DataImport, DifferentialExpression, ExperimentalDesign, GeneExpression, Microarray, Normalization, Preprocessing, SingleCell, Software, ThirdPartyClient |
| Package Short Url | https://bioconductor.org/packages/gemma.R/ |
Citation
From within R, enter citation("gemma.R"):
Javier Castillo-Arnemann, Jordan Sicherman, Ogan Mancarci, Guillaume Poirier-Morency, Paul Pavlidis. gemma.R: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses. doi:10.18129/B9.bioc.gemma.R, R package version 3.8.0, https://bioconductor.org/packages/gemma.R.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- A guide to metadata for samples and differential expression analyses
- A meta analysis on effects of Parkinson's Disease using Gemma.R
- Accessing curated gene expression data with gemma.R
Download
Follow the installation instructions to use this package in your R session.
| Source package | gemma.R_3.8.0.tar.gz |
| Windows binary (x86_64) | gemma.R_3.8.0.zip |
| macOS binary (arm64) | gemma.R_3.8.0.tgz |
| macOS binary (x86_64) | gemma.R_3.8.0.tgz |
Dependencies
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
Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, listviewer, shiny