Man pages for jsicherman/GemmAPI
A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

accessFieldAccess the field in a list
blank_processorA blank processor that returns data as is
checkBoundsReplace missing data with NAs
dot-getResultSetsRetrieve a single analysis result set by its identifier
encodeURL encode a string safely
filter_propertiesReturn all supported filter properties
forget_gemma_memoisedClear gemma.R cache
gemmaCacheGemma Cache
gemma_callCustom gemma call
gemma_kableCreate printable tables out of gemma.R outputs
gemma_memoiseEnable and disable memoisation of gemma.R functions
gemmaPathGet gemma path
gemma.Rgemma.R package: Access curated gene expression data and...
get_all_pagesGet all pages of a paginated call
get_child_termsReturn child terms of a term
get_dataset_annotationsRetrieve the annotations of a dataset
get_dataset_designRetrieve the design of a dataset
get_dataset_differential_expression_analysesRetrieve annotations and surface level stats for a dataset's...
get_dataset_expressionRetrieve processed expression data of a dataset
get_dataset_expression_for_genesRetrieve the expression data matrix of a set of datasets and...
get_dataset_objectCompile gene expression data and metadata
get_dataset_platformsRetrieve the platforms of a dataset
get_dataset_processed_expressionRetrieve processed expression data of a dataset
get_dataset_quantitation_typesRetrieve quantitation types of a dataset
get_dataset_raw_expressionRetrieve raw expression data of a dataset
get_datasetsRetrieve all datasets
get_dataset_samplesRetrieve the samples of a dataset
get_datasets_by_idsRetrieve datasets by their identifiers
get_differential_expression_valuesRetrieve differential expression results
get_gene_differential_expression_valuesRetrieve the differential expression results for a given gene...
get_gene_go_termsRetrieve the GO terms associated to a gene
get_gene_locationsRetrieve the physical locations of a given gene
get_gene_probesRetrieve the probes associated to a genes across all...
get_genesRetrieve genes matching gene identifiers
get_platform_annotationsRetrieve Platform Annotations by Gemma
get_platform_datasetsRetrieve all experiments using a given platform
get_platform_element_genesRetrieve the genes associated to a probe in a given platform
get_platforms_by_idsRetrieve all platforms matching a set of platform identifiers
get_result_setsRetrieve all result sets matching the provided criteria
get_taxaGet taxa
get_taxa_by_idsRetrieve taxa by their identifiers
get_taxon_datasetsRetrieve the datasets for a given taxon
isEmptyCheck for empty arguments
make_designMake simplified design frames
memoiseMemoise doc
nullCheckAvoid NULLS as data.table columns
processAnnotationsProcesses JSON as annotations
processCharacteristicValueObjectProcesses JSON as a factor
processDatasetResultSetsProcesses JSON as a datasets result set
processDatasetsProcesses JSON as a vector of datasets
processDEAProcesses JSON as a differential expression analysis
processDEcontrastsReplaces factor ids by the factors strings in DE table...
processDEMatrixProcesses differential expression matrix
processDesignMatrixProcesses design matrix
processDifferentialExpressionAnalysisResultByGeneValueObject_tsvprocessDifferentialExpressionAnalysisResultByGeneValueObject_tsv
processDifferentialExpressionAnalysisResultSetValueObjectProcess JSON of a result set
processElementsProcesses JSON as a vector of elements
processExpressionMatrixProcesses expression matrix
processFileProcesses a response as a gzip file
processGemmaArrayProcesses JSON as an array
processGeneLocationProcesses JSON as a vector of gene locations
processGenesProcesses JSON as a vector of genes
processGOProcesses JSON as GO terms
processPlatformsProcesses JSON as a vector of platforms
processQuantitationTypeValueObjectprocessQuantitationTypeValueObject
processResultSetFactorsProcesses JSON as a result set
processSamplesProcesses JSON as a vector of samples
process_searchReturns the ids of the found results
processSearchAnnotationsProcesses JSON as an annotation
processTaxonProcesses JSON as a vector of taxa
search_annotationsSearch for annotation tags
search_datasetsRetrieve datasets associated to an annotation tags search
search_gemmaSearch everything in Gemma
setGemmaPathSet gemma path
set_gemma_userAuthentication by user name
subset_factorValuesGet a subset of an array of factorValues
update_resultUpdate result
validateBooleanValidate a boolean value
validateIDValidate identifiers (ie. gene ID, platform ID, etc.) that...
validateLimitValidate a limit value
validateOptionalIDValidate identifiers (ie. gene ID, platform ID, etc.) that...
validateOptionalQueryValidate am optional query
validateOptionalTaxonValidate a taxon using the acceptable taxa entries
validatePositiveIntegerValidate a non-negative integer value
validateQueryValidate a query
validateResultTypeValidate result types
validateSingleIDValidate a single identifier(ie. gene ID, platform ID, etc.)
validateSortValidate a sort argument
validateTaxaValidate taxa using the acceptable taxa entries
validateTaxonValidate a taxon using the acceptable taxa entries
jsicherman/GemmAPI documentation built on Dec. 15, 2024, 8:59 a.m.