supercell_tSNE

Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells. 'SuperCell' uses 'velocyto.R' <doi:10.1038/s41586-018-0414-6> <https://github.com/velocyto-team/velocyto.R> for RNA velocity. We also recommend installing 'scater' Bioconductor package <doi:10.18129/B9.bioc.scater> <https://bioconductor.org/packages/release/bioc/html/scater.html>.

Leonard Herault

SuperCell

Simplification of scRNA-Seq Data by Merging Together Similar
Cells

Mariia Bilous

supercell_tSNE function

<dl><dt>SC</dt>
<dd>super-cell structure (output of SCimplify) with a field <code>PCA_name</code> containig PCA result</dd>
<dt>PCA_name</dt>
<dd>name of <code>SC</code> field containing result of supercell_prcomp</dd>
<dt>n.comp</dt>
<dd>number of vector of principal components to use for computing tSNE</dd>
<dt>perplexity</dt>
<dd>perplexity parameter (parameter of Rtsne)</dd>
<dt>seed</dt>
<dd>random seed</dd>
<dt>...</dt>
<dd>other parameters of Rtsne</dd></dl>

Arguments

Compute tSNE of super-cells — supercell_tSNE

<dl>

<dt>SC</dt>
<dd>super-cell structure (output of SCimplify) with a field <code>PCA_name</code> containig PCA result</dd>


<dt>PCA_name</dt>
<dd>name of <code>SC</code> field containing result of supercell_prcomp</dd>


<dt>n.comp</dt>
<dd>number of vector of principal components to use for computing tSNE</dd>


<dt>perplexity</dt>
<dd>perplexity parameter (parameter of Rtsne)</dd>


<dt>seed</dt>
<dd>random seed</dd>


<dt>...</dt>
<dd>other parameters of Rtsne</dd>

</dl>

supercell_tSNE: Compute tSNE of super-cells

Description

Usage

Value

Arguments