# A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

## Documentation for package ‘gemma.R’ version 3.8.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

gemma.R-package | gemma.R package: Access curated gene expression data and differential expression analyses
filter_properties | Return all supported filter properties
forget_gemma_memoised | Clear gemma.R cache
gemma.R | gemma.R package: Access curated gene expression data and differential expression analyses
gemma_call | Custom gemma call
gemma_kable | Create printable tables out of gemma.R outputs
gemma_memoise | Enable and disable memoisation of gemma.R functions
get_all_pages | Get all pages of a paginated call
get_annotation_children | Retrieve children of a given annotation
get_annotation_parents | Retrieve parents of a given annotation
get_child_terms | Return child terms of a term
get_datasets | Retrieve all datasets
get_datasets_by_ids | Retrieve datasets by their identifiers
get_dataset_annotations | Retrieve the annotations of a dataset
get_dataset_differential_expression_analyses | Retrieve annotations and surface level stats for a dataset's differential analyses
get_dataset_expression_for_genes | Retrieve the expression data matrix of a set of datasets and genes
get_dataset_object | Compile gene expression data and metadata
get_dataset_platforms | Retrieve the platforms of a dataset
get_dataset_processed_expression | Retrieve processed expression data of a dataset
get_dataset_publications | Retrieve all publications associated with a dataset
get_dataset_quantitation_types | Retrieve quantitation types of a dataset
get_dataset_raw_expression | Retrieve raw expression data of a dataset
get_dataset_samples | Retrieve the samples of a dataset
get_differential_expression_values | Retrieve differential expression results
get_genes | Retrieve all genes
get_gene_differential_expression_values | Retrieve the differential expression results for a given gene among datasets matching the provided query and filter
get_gene_go_terms | Retrieve the GO terms associated to a gene
get_gene_locations | Retrieve the physical locations of a given gene
get_gene_probes | Retrieve the probes associated to a genes across all platforms
get_platforms_by_ids | Retrieve all platforms matching a set of platform identifiers
get_platform_annotations | Retrieve Platform Annotations by Gemma
get_platform_datasets | Retrieve all experiments using a given platform
get_platform_element_genes | Retrieve the genes associated to a probe in a given platform
get_result_sets | Retrieve all result sets matching the provided criteria
get_taxa | Get taxa
make_design | Make simplified design frames
search_annotations | Search for annotation tags
search_gemma | Search everything in Gemma
set_gemma_user | Authentication by user name
update_result | Update result