ExtractRun

Extract Runs with GEO Accession Number or GSM Number.

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

ExtractRun function

<dl><dt>gsm</dt>
<dd>GSM number. Default: NULL (use <code>acce</code>).</dd>
<dt>acce</dt>
<dd>GEO accession number. Default: NULL (use <code>gsm</code>).
<code>acce</code> and <code>gsm</code> cannot be both NULL.</dd>
<dt>platform</dt>
<dd>Platform information/field. Default: NULL (all platforms).</dd>
<dt>parallel</dt>
<dd>Logical value, whether to process GSM parallelly. Default: TRUE.</dd>
<dt>...</dt>
<dd>Parameters for <code>getGEO</code>. Used when <code>acce</code> is not NULL.</dd></dl>

Arguments

Extract Runs with GEO Accession Number or GSM Number. — ExtractRun

<dl>

<dt>gsm</dt>
<dd>GSM number. Default: NULL (use <code>acce</code>).</dd>


<dt>acce</dt>
<dd>GEO accession number. Default: NULL (use <code>gsm</code>).
<code>acce</code> and <code>gsm</code> cannot be both NULL.</dd>


<dt>platform</dt>
<dd>Platform information/field. Default: NULL (all platforms).</dd>


<dt>parallel</dt>
<dd>Logical value, whether to process GSM parallelly. Default: TRUE.</dd>


<dt>...</dt>
<dd>Parameters for <code>getGEO</code>. Used when <code>acce</code> is not NULL.</dd>

</dl>

ExtractRun: Extract Runs with GEO Accession Number or GSM Number.

Description

Usage

Value

Arguments

Examples