getSampleList: Get the sample list from the panglaoDB database.

In rPanglaoDB: Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Database

Description

Get the sample list from the panglaoDB database.

Usage

getSampleList()

Value

This function returns a data frame with 6 columns as follows:

• SRA: The SRA identifier of the biological sample in the SRA database

• SRS: The SRS identifier of the biological sample in the SRA database

• Tissue: The tissue from which the biological samples originated from

• Protocol: The single-cell library preparation protocol used to generate the data

• Species: The specie from which the biological samples originated from

• Cells: The number of cells included in the sample

Examples

# From the PanglaoDB database
# https://panglaodb.se/samples.html

sampleList <- getSampleList()
head(sampleList)

#       SRA        SRS                          Tissue     Protocol      Species Cells
# SRA553822 SRS2119548   Cultured embryonic stem cells 10x chromium Homo sapiens  6501
# SRA570744 SRS2253536                 Lung mesenchyme 10x chromium Mus musculus  4611
# SRA598936 SRS2428405                   Kidney cortex 10x chromium Homo sapiens  3759
# SRA644036 SRS2808714 Cervical and lumbar spinal cord 10x chromium Mus musculus  1025
# SRA670243 SRS3078084                Ventral midbrain 10x chromium Mus musculus  5603
# SRA689041 SRS3166675                           Colon 10x chromium Mus musculus  2878

rPanglaoDB documentation built on May 13, 2021, 1:07 a.m.