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##
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## union, unique, unsplit, which.max, which.min## Loading required package: AnnotationHub## Loading required package: BiocFileCache## Loading required package: dbplyrlibrary(SingleCellExperiment)## Loading required package: SummarizedExperiment## Loading required package: MatrixGenerics## Loading required package: matrixStats##
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## I, expand.grid, unname## Loading required package: IRanges## Loading required package: GenomeInfoDb## Loading required package: Biobase## Welcome to Bioconductor
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## cacheeh = ExperimentHub()
dset <- query(eh , "GSE103322")
dset## ExperimentHub with 1 record
## # snapshotDate(): 2024-04-29
## # 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
## # $tags: c("CancerData", "DNASeqData", "ExpressionData", "Genome",
## # "GEO", "Homo_sapiens_Data", "RNASeqData", "SingleCellData")
## # retrieve record with 'object[["EH5419"]]'One can then extract the data for this using
sce <- dset[[1]]## see ?GSE103322 and browseVignettes('GSE103322') for documentation## loading from cacheThe metadata is available from the SingleCellExpression object with
head(SummarizedExperiment::colData(sce))## DataFrame with 6 rows and 5 columns
## processed.by.Maxima.enzyme Lymph.node
## <character> <character>
## HN28_P15_D06_S330_comb 1 1
## HN28_P6_G05_S173_comb 1 0
## HN26_P14_D11_S239_comb 1 1
## HN26_P14_H05_S281_comb 1 1
## HN26_P25_H09_S189_comb 1 1
## HN26_P14_H06_S282_comb 1 1
## classified..as.cancer.cell
## <character>
## HN28_P15_D06_S330_comb 0
## HN28_P6_G05_S173_comb 0
## HN26_P14_D11_S239_comb 1
## HN26_P14_H05_S281_comb 0
## HN26_P25_H09_S189_comb 1
## HN26_P14_H06_S282_comb 1
## classified.as.non.cancer.cells non.cancer.cell.type
## <character> <character>
## HN28_P15_D06_S330_comb 1 Fibroblast
## HN28_P6_G05_S173_comb 1 Fibroblast
## HN26_P14_D11_S239_comb 0 0
## HN26_P14_H05_S281_comb 1 Fibroblast
## HN26_P25_H09_S189_comb 0 0
## HN26_P14_H06_S282_comb 0 0For example, to obtain the number of cells classified as non-tumor types
table(SummarizedExperiment::colData(sce)$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 version 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
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## time zone: America/New_York
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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_1.10.0 GEOquery_2.72.0
## [3] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0
## [5] Biobase_2.64.0 GenomicRanges_1.56.0
## [7] GenomeInfoDb_1.40.0 IRanges_2.38.0
## [9] S4Vectors_0.42.0 MatrixGenerics_1.16.0
## [11] matrixStats_1.3.0 ExperimentHub_2.12.0
## [13] AnnotationHub_3.12.0 BiocFileCache_2.12.0
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