Transcripts per million (TPM) single cell RNA-Seq data for 5,902 cells from 18 patients–oral cavity head and neck squamous cell carcinoma (HNSC)– are available from GEO GSE103322. These data are also available as a SingleCellExpression from ExperimentHub.
In the example below, we show how this dataset can be dwnloaded from ExperimentHub.
library(ExperimentHub)## Loading required package: BiocGenerics## Loading required package: generics##
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## cacheeh = ExperimentHub()
dset <- query(eh , "GSE103322")
dset## ExperimentHub with 1 record
## # snapshotDate(): 2025-10-10
## # names(): EH5419
## # package(): GSE103322
## # $dataprovider: GEO
## # $species: Homo sapiens
## # $rdataclass: SingleCellExperiment
## # $rdatadateadded: 2021-03-04
## # $title: Single cell RNA-seq data for human head and neck squamous cell car...
## # $description: scRNA-Sequencing data and metadata for 5902 cells from 18 p...
## # $taxonomyid: 9606
## # $genome: hg19
## # $sourcetype: tar.gz
## # $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103322
## # $sourcesize: NA
## # $tags: c("CancerData", "DNASeqData", "ExpressionData", "Genome",
## # "GEO", "Homo_sapiens_Data", "RNASeqData", "SingleCellData")
## # retrieve record with 'object[["EH5419"]]'One can then extract the data for this using
sce <- dset[[1]]## Setting options('download.file.method.GEOquery'='auto')## Setting options('GEOquery.inmemory.gpl'=FALSE)## see ?GSE103322 and browseVignettes('GSE103322') for documentation## loading from cacheThe metadata is available from the SingleCellExpression object with
head(SummarizedExperiment::colData(sce))## DataFrame with 6 rows and 5 columns
## processed.by.Maxima.enzyme Lymph.node
## <character> <character>
## HN28_P15_D06_S330_comb 1 1
## HN28_P6_G05_S173_comb 1 0
## HN26_P14_D11_S239_comb 1 1
## HN26_P14_H05_S281_comb 1 1
## HN26_P25_H09_S189_comb 1 1
## HN26_P14_H06_S282_comb 1 1
## classified..as.cancer.cell
## <character>
## HN28_P15_D06_S330_comb 0
## HN28_P6_G05_S173_comb 0
## HN26_P14_D11_S239_comb 1
## HN26_P14_H05_S281_comb 0
## HN26_P25_H09_S189_comb 1
## HN26_P14_H06_S282_comb 1
## classified.as.non.cancer.cells non.cancer.cell.type
## <character> <character>
## HN28_P15_D06_S330_comb 1 Fibroblast
## HN28_P6_G05_S173_comb 1 Fibroblast
## HN26_P14_D11_S239_comb 0 0
## HN26_P14_H05_S281_comb 1 Fibroblast
## HN26_P25_H09_S189_comb 0 0
## HN26_P14_H06_S282_comb 0 0For example, to obtain the number of cells classified as non-tumor types
table(SummarizedExperiment::colData(sce)$non.cancer.cell.type)##
## -Fibroblast 0 B cell Dendritic Endothelial Fibroblast
## 18 2539 138 51 260 1422
## Macrophage Mast T cell myocyte
## 98 120 1237 19The data can be extracted from the SingleCellExpression object with
dset <- SummarizedExperiment::assays(sce)$TPM
dim(dset)## [1] 21341 5902dset[1:4, 1:3]## HN28_P15_D06_S330_comb HN28_P6_G05_S173_comb HN26_P14_D11_S239_comb
## 401546 0.0000 0.0000 0.42761
## 6205 6.0037 7.3006 7.28850
## 63916 0.0000 0.0000 0.00000
## 90993 0.0000 0.0000 0.00000sessionInfo()## R Under development (unstable) (2025-10-20 r88955)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
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## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
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## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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## time zone: America/New_York
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
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## other attached packages:
## [1] GSE103322_1.15.0 GEOquery_2.77.6
## [3] SingleCellExperiment_1.31.1 SummarizedExperiment_1.39.2
## [5] Biobase_2.69.1 GenomicRanges_1.61.6
## [7] Seqinfo_0.99.3 IRanges_2.43.5
## [9] S4Vectors_0.47.4 MatrixGenerics_1.21.0
## [11] matrixStats_1.5.0 ExperimentHub_2.99.6
## [13] AnnotationHub_3.99.6 BiocFileCache_2.99.6
## [15] dbplyr_2.5.1 BiocGenerics_0.55.4
## [17] generics_0.1.4 BiocStyle_2.37.1
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## [64] BiocManager_1.30.26 jsonlite_2.0.0 R6_2.6.1