A subsetted version of human 'panc8' datasets

Human pancreatic islet cell datasets produced across four technologies, CelSeq (GSE81076) CelSeq2 (GSE85241), Fluidigm C1 (GSE86469), and SMART-Seq2 (E-MTAB-5061) from SeuratData package. For each data set in `panc8`, 200 cells were downsampled to form the panc8_sub dataset.

Format

A Seurat object.

Source

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81076 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5061/ https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi

Examples

if (FALSE) { # \dontrun{
if (interactive()) {
  data("pancreas_sub")
  if (!require("SeuratData", quietly = TRUE)) {
    pak::pak("satijalab/seurat-data")
  }
  library(SeuratData)
  library(Seurat)
  suppressWarnings(InstallData("panc8"))
  data("panc8")
  panc8 <- Seurat::UpdateSeuratObject(panc8)
  set.seed(11)
  cells_sub <- unlist(
    lapply(
      split(colnames(panc8), panc8$dataset),
      function(x) sample(x, size = 200)
    )
  )
  panc8_sub <- subset(panc8, cells = cells_sub)
  counts <- GetAssayData5(
    panc8_sub,
    slot = "counts"
  )
  panc8_sub <- Seurat::CreateSeuratObject(
    counts = counts,
    meta.data = panc8_sub@meta.data
  )
  panc8_sub <- panc8_sub[Matrix::rowSums(counts) > 0, ]
  panc8_sub <- panc8_sub[toupper(
    rownames(panc8_sub)
  ) %in% toupper(
    rownames(pancreas_sub)
  ), ]
  panc8_sub$celltype <- gsub("_", "-", panc8_sub$celltype)
  panc8_sub$celltype <- gsub(" ", "-", panc8_sub$celltype)
  panc8_sub <- Seurat::NormalizeData(panc8_sub, verbose = FALSE)
  panc8_sub <- Seurat::FindVariableFeatures(
    panc8_sub,
    verbose = FALSE
  )
  panc8_sub <- Seurat::ScaleData(panc8_sub, verbose = FALSE)
  panc8_sub <- Seurat::RunPCA(panc8_sub, verbose = FALSE)
  panc8_sub <- Seurat::RunUMAP(
    panc8_sub,
    dims = 1:30,
    verbose = FALSE
  )
  panc8_sub <- Seurat::RunTSNE(
    panc8_sub,
    dims = 1:30,
    verbose = FALSE
  )
  usethis::use_data(
    panc8_sub,
    compress = "xz",
    overwrite = TRUE
  )
}
} # }