panc8_sub: A subsetted version of human 'panc8' datasets
In zh542370159/SCP: Single Cell Pipeline

panc8_sub

R Documentation

A subsetted version of human 'panc8' datasets

Description

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

## Not run: 
if (interactive()) {
  data("pancreas_sub")
  if (!require("SeuratData", quietly = TRUE)) {
    devtools::install_github("satijalab/seurat-data")
  }
  library(SeuratData)
  library(Seurat)
  suppressWarnings(InstallData("panc8"))
  data("panc8")
  set.seed(11)
  cells_sub <- unlist(lapply(split(colnames(panc8), panc8$dataset), function(x) sample(x, size = 200)))
  panc8_sub <- subset(panc8, cells = cells_sub)
  panc8_sub <- panc8_sub[rowSums(panc8_sub@assays$RNA@counts) > 0, ]
  panc8_sub <- panc8_sub[toupper(rownames(panc8_sub)) %in% toupper(rownames(pancreas_sub)), ]
  panc8_sub <- UpdateSeuratObject(panc8_sub)
  # usethis::use_data(panc8_sub, compress = "xz")
}

## End(Not run)

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.