getAtlasSCExperiment: Download data for a Single-Cell Expression Atlas experiment

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

Download data for a Single-Cell Expression Atlas experiment

Description

This function downloads and returns a SingleCellExperiment object representing a Single-Cell Expression Atlas experiment.

Usage

    getAtlasSCExperiment( experimentAccession )

Arguments

experimentAccession

Single-cell experiment accession e.g. "E-ENAD-19"

Value

A SingleCellExperiment object representing a single-Cell Expression Atlas experiment.

Each SCE object contains the following:

• Assays, containing the raw counts (X), filtered counts (filtered), and normalised and filtered counts (normalised).

• Column data (cell-level metadata)

• Different dimensionality reductions (e.g. PCA, t-SNE, UMAP)

Examples

    
    # Download the experiment summary for E-GEOD-11175
    enad19 <- getAtlasSCExperiment( "E-ENAD-19" )

    enad19
    # Prints out the following:
    #
    # class: SingleCellExperiment 
    # dim: 3644 26 
    # metadata(0):
    # assays(3): X filtered normalised
    # rownames: NULL
    # rowData names(1): PCs
    # colnames(26): ERR2192535 ERR2192536 ... ERR2192559 ERR2192560
    # colData names(27): age cell_type ... louvain_resolution_1.0
    #   louvain_resolution_2.0
    # reducedDimNames(21): X_pca X_tsne_perplexity_1 ...
    #   X_umap_neighbors_n_neighbors_5 X_umap_neighbors_n_neighbors_50
    # mainExpName: NULL
    # altExpNames(0):

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