Name Mode Size
..
figures 040000
accessField.Rd 100644 1 kb
blank_processor.Rd 100644 0 kb
checkBounds.Rd 100644 0 kb
dot-getResultSetFactors.Rd 100644 2 kb
dot-getResultSets.Rd 100644 2 kb
encode.Rd 100644 0 kb
forget_gemma_memoised.Rd 100644 0 kb
gemma.R.Rd 100644 2 kb
gemmaCache.Rd 100644 0 kb
gemmaPath.Rd 100644 0 kb
gemma_call.Rd 100644 1 kb
get_dataset_annotations.Rd 100644 2 kb
get_dataset_design.Rd 100644 2 kb
get_dataset_differential_expression_analyses.Rd 100644 4 kb
get_dataset_expression.Rd 100644 2 kb
get_dataset_object.Rd 100644 2 kb
get_dataset_platforms.Rd 100644 3 kb
get_dataset_samples.Rd 100644 2 kb
get_datasets_by_ids.Rd 100644 5 kb
get_differential_expression_values.Rd 100644 3 kb
get_gene_go_terms.Rd 100644 2 kb
get_gene_locations.Rd 100644 2 kb
get_gene_probes.Rd 100644 3 kb
get_genes.Rd 100644 2 kb
get_platform_annotations.Rd 100644 2 kb
get_platform_datasets.Rd 100644 4 kb
get_platform_element_genes.Rd 100644 3 kb
get_platforms_by_ids.Rd 100644 3 kb
get_result_sets.Rd 100644 2 kb
get_taxa.Rd 100644 1 kb
get_taxa_by_ids.Rd 100644 3 kb
get_taxon_datasets.Rd 100644 6 kb
nullCheck.Rd 100644 0 kb
processAnnotations.Rd 100644 1 kb
processDEA.Rd 100644 2 kb
processDEMatrix.Rd 100644 0 kb
processDEcontrasts.Rd 100644 0 kb
processDatasetResultSets.Rd 100644 1 kb
processDatasets.Rd 100644 3 kb
processDesignMatrix.Rd 100644 0 kb
processElements.Rd 100644 1 kb
processExpressionMatrix.Rd 100644 0 kb
processFile.Rd 100644 0 kb
processGO.Rd 100644 1 kb
processGemmaArray.Rd 100644 0 kb
processGemmaFactor.Rd 100644 0 kb
processGeneLocation.Rd 100644 1 kb
processGenes.Rd 100644 1 kb
processPlatforms.Rd 100644 1 kb
processResultSetFactors.Rd 100644 0 kb
processSamples.Rd 100644 1 kb
processSearchAnnotations.Rd 100644 1 kb
processTaxon.Rd 100644 1 kb
process_search.Rd 100644 0 kb
search_annotations.Rd 100644 2 kb
search_datasets.Rd 100644 6 kb
search_gemma.Rd 100644 3 kb
set_gemma_user.Rd 100644 1 kb
validateBoolean.Rd 100644 0 kb
validateID.Rd 100644 1 kb
validateLimit.Rd 100644 0 kb
validateOptionalID.Rd 100644 1 kb
validateOptionalTaxon.Rd 100644 0 kb
validatePositiveInteger.Rd 100644 0 kb
validateQuery.Rd 100644 0 kb
validateResultType.Rd 100644 0 kb
validateSingleID.Rd 100644 0 kb
validateSort.Rd 100644 0 kb
validateTaxa.Rd 100644 0 kb
validateTaxon.Rd 100644 0 kb
README.Rmd
--- output: github_document --- ```{r, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" ) ``` # gemma.R: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses <img src='man/figures/logo.png' align="right" height="138" /> <!-- badges: start --> [![R build status](https://github.com/PavlidisLab/gemma.R/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/PavlidisLab/gemma.R/actions) [![Codecov test coverage](https://codecov.io/gh/PavlidisLab/gemma.R/branch/master/graph/badge.svg)](https://codecov.io/gh/PavlidisLab/gemma.R?branch=master) [![DOI](https://img.shields.io/badge/doi-10.1093/database/baab006-yellow.svg)](https://doi.org/10.1093/database/baab006) <!-- badges: end --> This is an R wrapper for [Gemma](http://gemma.msl.ubc.ca)’s RESTful [API](https://gemma.msl.ubc.ca/rest/v2/). 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. Gemma contains data from thousands of public studies, referencing thousands of published papers. ## Installation instructions ### Bioconductor You can install `gemma.R` through [Bioconductor](http://bioconductor.org/) with the following code: ```{r 'install', eval = FALSE} if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } # The following initializes usage of Bioc devel # it won't be necessary with the next version # of Bioconductor BiocManager::install(version='devel') BiocManager::install("gemma.R") ``` ## Usage To get started with `gemma.R`, read the [vignette](https://pavlidislab.github.io/gemma.R/articles/gemma.R.html). ## Citation To cite Gemma, please use: [Lim, N. et al., Curation of over 10 000 transcriptomic studies to enable data reuse, Database, 2021.](https://doi.org/10.1093/database/baab006) ## Code of Conduct Please note that `gemma.R` is released with the [Bioconductor Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.