PanglaoDBMeta

A dataset contains all sample metadata and cell types of PanglaoDB datasets.

datasets

The goal of 'scfetch' is to access and format single-cell RNA-seq datasets. It can be used to download single-cell RNA-seq
datasets from widely used public resources, including GEO <https://www.ncbi.nlm.nih.gov/geo/>, Zenodo <https://zenodo.org/>,
CELLxGENE <https://cellxgene.cziscience.com/>, Human Cell Atlas <https://www.humancellatlas.org/>, PanglaoDB <https://panglaodb.se/index.html>
and UCSC Cell Browser <https://cells.ucsc.edu/>. And, it can also be used to perform object conversion between SeuratObject <https://satijalab.org/seurat/>,
loom <http://loompy.org/>, h5ad <https://scanpy.readthedocs.io/en/stable/>, SingleCellExperiment <https://bioconductor.org/packages/release/bioc/html/scran.html>,
CellDataSet <http://cole-trapnell-lab.github.io/monocle-release/> and cell_data_set <https://cole-trapnell-lab.github.io/monocle3/>.

Yabing Song

scfetch

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

PanglaoDBMeta function

A data frame with 1,368 rows and 7 variables:<dl>
 <dt>SRA</dt>
<dd>The SRA identifier</dd> <dt>SRS</dt>
<dd>The SRS identifier</dd> <dt>Tissue</dt>
<dd>The tissue of the sample</dd> <dt>Protocol</dt>
<dd>The protocol used to generate this sample</dd> <dt>Species</dt>
<dd>The species of this sample</dd> <dt>Cells</dt>
<dd>Total cell number of this sample</dd> <dt>CellType</dt>
<dd>Predicted cell types, separated by comma</dd>
</dl>

Format

All Sample Metadata of PanglaoDB Datasets — PanglaoDBMeta

A data frame with 1,368 rows and 7 variables:<dl>
 <dt>SRA</dt>
<dd>The SRA identifier</dd>

 <dt>SRS</dt>
<dd>The SRS identifier</dd>

 <dt>Tissue</dt>
<dd>The tissue of the sample</dd>

 <dt>Protocol</dt>
<dd>The protocol used to generate this sample</dd>

 <dt>Species</dt>
<dd>The species of this sample</dd>

 <dt>Cells</dt>
<dd>Total cell number of this sample</dd>

 <dt>CellType</dt>
<dd>Predicted cell types, separated by comma</dd>


</dl>

PanglaoDBMeta: All Sample Metadata of PanglaoDB Datasets

Description

Usage

Arguments

Format