supercell_GE_idx

This function converts gene-expression matrix of single-cell data into a gene expression
matrix of super-cells

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_GE_idx function

<dl><dt>ge</dt>
<dd>gene expression matrix (or any coordinate matrix) with genes as rows and cells as cols</dd>
<dt>groups</dt>
<dd>vector of membership (assignment of single-cell to super-cells)</dd>
<dt>weights</dt>
<dd>vector of a cell weight (NULL by default), used for computing average gene expression withing cluster of super-cells</dd>
<dt>do.median.norm</dt>
<dd>whether to normalize by median value (FALSE by default)</dd></dl>

Arguments

Simplification of scRNA-seq dataset (old version, not used since 12.02.2021) — supercell_GE_idx

<dl>

<dt>ge</dt>
<dd>gene expression matrix (or any coordinate matrix) with genes as rows and cells as cols</dd>


<dt>groups</dt>
<dd>vector of membership (assignment of single-cell to super-cells)</dd>


<dt>weights</dt>
<dd>vector of a cell weight (NULL by default), used for computing average gene expression withing cluster of super-cells</dd>


<dt>do.median.norm</dt>
<dd>whether to normalize by median value (FALSE by default)</dd>

</dl>

supercell_GE_idx: Simplification of scRNA-seq dataset (old version, not used since 12.02.2021)

Description

Usage

Value

Arguments