ExtractGEOExpSupp10x

Fortmat Supplementary Files to 10x.

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

ExtractGEOExpSupp10x function

<dl><dt>acce</dt>
<dd>GEO accession number.</dd>
<dt>supp.idx</dt>
<dd>The index of supplementary files to download. Default: 1.</dd>
<dt>timeout</dt>
<dd>Timeout for <code><a href="/link/download.file?package=scfetch&version=0.5.0" data-mini-rdoc="scfetch::download.file">download.file</a></code>. Default: 3600.</dd>
<dt>out.folder</dt>
<dd>Output folder to save 10x files. Default: NULL (current working directory).</dd>
<dt>gene2feature</dt>
<dd>Logical value, whether to rename <code>genes.tsv.gz</code> to <code>features.tsv.gz</code>.
Default: TURE.</dd></dl>

Arguments

Fortmat Supplementary Files to 10x. — ExtractGEOExpSupp10x

<dl>

<dt>acce</dt>
<dd>GEO accession number.</dd>


<dt>supp.idx</dt>
<dd>The index of supplementary files to download. Default: 1.</dd>


<dt>timeout</dt>
<dd>Timeout for <code><a href='https://rdrr.io/r/utils/download.file.html'>download.file</a></code>. Default: 3600.</dd>


<dt>out.folder</dt>
<dd>Output folder to save 10x files. Default: NULL (current working directory).</dd>


<dt>gene2feature</dt>
<dd>Logical value, whether to rename <code>genes.tsv.gz</code> to <code>features.tsv.gz</code>.
Default: TURE.</dd>

</dl>

ExtractGEOExpSupp10x: Fortmat Supplementary Files to 10x.

Description

Usage

Arguments