searchAtlasExperiments: Search for Expression Atlas experiments

In ebi-gene-expression-group/bioconductor-ExpressionAtlas: Search, download and visualise datasets from EMBL-EBI Expression Atlas and Single-Cell Expression Atlas

Search for Expression Atlas experiments

Description

This function accepts a query, and optionally a secondary filter, and then searches for matching Expression Atlas experiments in the EBI RESTful Web Services API

Usage

    searchAtlasExperiments( query, secondaryFilter = NULL, detailed = FALSE  )

Arguments

query	Character of sample properties to search Atlas for. These can be biological characteristics, experimental treatments, species, etc.
secondaryFilter	Optional, a second filter.
detailed	If TRUE, it will perform a detailed search through Atlas experiment metadata information, and it might take 10-20 seconds. Default: FALSE.

Value

A DataFrame containing the Expression Atlas accessions, the species, experiment types, and titles of Expression Atlas experiments matching the query.

Examples

    # Search for endoderm experiments (4 results)
    atlasRes_1 <- searchAtlasExperiments( query="endoderm")

    # Search for endoderm experiments in human (2 results)
    atlasRes_2 <- searchAtlasExperiments( query="endoderm", secondaryFilter = "human" )
    # it produces same results as:
    # atlasRes_2 <- searchAtlasExperiments( query="human", secondaryFilter = "endoderm" )

    # Download data for first experiment found.
    if ( nrow( atlasRes_2 ) == 1 ) {
        atlasData <- getAtlasData( atlasRes_2$Accession )
    } else {
        atlasData <- getAtlasData( atlasRes_2$Accession[1] )
    }

ebi-gene-expression-group/bioconductor-ExpressionAtlas documentation built on July 4, 2025, 12:53 a.m.