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

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Documentation for package ‘gemma.R’ version 3.0.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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_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_design	Retrieve the design 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_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 genes matching gene identifiers
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