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

This vignette demonstrates how to access and visualise data from the Single-Cell Expression Atlas using the ExpressionAtlas package.

knitr::opts_chunk$set(message=FALSE)
knitr::opts_chunk$set(warning=FALSE)

library( ExpressionAtlas ) 

sc_search_results <- searchSCAtlasExperiments( query = "hematopoietic", secondaryFilter = "old" )
print(sc_search_results)

geod87631 <- getAtlasSCExperiment( "E-GEOD-87631" )
geod87631

print("Reduced dimension names:")
print(reducedDimNames(geod87631 ))

print("Column data names:")
print(colnames(colData(geod87631 )))

plotDimRedSCAtlasExperiment(geod87631, dimRed = "X_umap_neighbors_n_neighbors_20", colorby = "louvain_resolution_0.1") + theme_classic() 

plotDimRedSCAtlasExperiment(geod87631, dimRed = "X_umap_neighbors_n_neighbors_20", colorby = "cell_type") + theme_classic() 

plotDimRedSCAtlasExperiment(geod87631, dimRed = "X_umap_neighbors_n_neighbors_20", colorby = "age") + theme_classic() 

plotDimRedSCAtlasExperiment(geod87631, dimRed = "X_umap_neighbors_n_neighbors_20", colorby = "genotype") + theme_classic() 


heatmapSCAtlasExperiment(geod87631, genes=NULL, sel.K=5, scaleNormExp=FALSE, show_row_names=FALSE ) 

heatmapSCAtlasExperiment(geod87631, genes=NULL, sel.K=5, scaleNormExp=TRUE, show_row_names=FALSE ) 

# random genes
dotPlotSCAtlasExperiment(geod87631, genes=c('ENSMUSG00000056758', 'ENSMUSG00000076867', 'ENSMUSG00000022584', 'ENSMUSG00000048442'), sel.K=5, scaleNormExp=TRUE) + theme_classic()

# random genes
dotPlotSCAtlasExperiment(geod87631, genes=c('ENSMUSG00000056758', 'ENSMUSG00000076867', 'ENSMUSG00000022584', 'ENSMUSG00000048442'), sel.K=9, scaleNormExp=FALSE) + theme_classic()

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