ExtractPanglaoDBComposition: Extract Cell Type Composition of PanglaoDB Datasets.

In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

Extract Cell Type Composition of PanglaoDB Datasets.

Description

Extract Cell Type Composition of PanglaoDB Datasets.

Usage

ExtractPanglaoDBComposition(
  sra = NULL,
  srs = NULL,
  species = NULL,
  protocol = NULL,
  tissue = NULL,
  local.data = TRUE
)

Arguments

sra	The SRA identifier of the datasets, obtain available values with StatDBAttribute, one or multiple value. Default: NULL (All).
srs	The SRS identifier of the datasets, obtain available values with StatDBAttribute, one or multiple value. Default: NULL (All).
species	The species of the datasets, choose from "Homo sapiens", "Mus musculus", one or multiple value. Default: NULL (All).
protocol	Protocol used to generate the datasets, choose from "10x chromium", "drop-seq", "microwell-seq", "C1 Fluidigm", "inDrops", "Smart-seq2", "CEL-seq", one or multiple value. Default: NULL (All).
tissue	The tissue of the datasets, obtain available values with StatDBAttribute, one or multiple value. Default: NULL (All).
local.data	Logical value, whether to use local data (PanglaoDB is no longer maintained). Default: TRUE.

Value

Dataframe contains sample metadata, cluster, cell number and cell type information.

Examples

human.composition <- ExtractPanglaoDBComposition(
  species = "Homo sapiens",
  protocol = c("Smart-seq2", "10x chromium")
)

scfetch documentation built on Nov. 22, 2023, 1:09 a.m.