searchSCAtlasExperiments: Search for Sinle-Cell 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 Sinle-Cell Expression Atlas experiments

Description

This function accepts a query, and optionally a secondary filter, and then searches for matching Single-Cell Expression Atlas experiments in the EBI RESTful Web Services API. The function also performs ontology-based query search against the Single Cell Expression Atlas cell-type wheel.

Usage

    searchSCAtlasExperiments( query, secondaryFilter = NULL  )

Arguments

query	Character of sample properties to search Atlas for. These can be biological characteristics, experimental treatments, species, etc.
secondaryFilter	Optional, a second filter. For instance, if the query is "lung", the secondary filter can be "human" to search for human lung experiments.

Value

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

Examples

    # Search for pancreas experiments
    atlasRes_pancreas <- searchSCAtlasExperiments( query="pancreas")

    # Search for human lung experiments
    atlasRes_human_lung <- searchSCAtlasExperiments( query="lung", secondaryFilter = "human")

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