SCimplify_for_velocity

Construct super-cells from spliced and un-spliced matrices

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

SCimplify_for_velocity function

<dl><dt>emat</dt>
<dd>spliced (exonic) count matrix</dd>
<dt>nmat</dt>
<dd>unspliced (nascent) count matrix</dd>
<dt>gamma</dt>
<dd>graining level of data (proportion of number of single cells in the initial dataset to the number of super-cells in the final dataset)</dd>
<dt>membership</dt>
<dd>metacell membership vector (if provided, will be used for <code>emat</code>, <code>nmat</code> metacell matrices averaging)</dd>
<dt>...</dt>
<dd>other parameters from SCimplify</dd></dl>

Arguments

Construct super-cells from spliced and un-spliced matrices — SCimplify_for_velocity

<dl>

<dt>emat</dt>
<dd>spliced (exonic) count matrix</dd>


<dt>nmat</dt>
<dd>unspliced (nascent) count matrix</dd>


<dt>gamma</dt>
<dd>graining level of data (proportion of number of single cells in the initial dataset to the number of super-cells in the final dataset)</dd>


<dt>membership</dt>
<dd>metacell membership vector (if provided, will be used for <code>emat</code>, <code>nmat</code> metacell matrices averaging)</dd>


<dt>...</dt>
<dd>other parameters from SCimplify</dd>

</dl>

SCimplify_for_velocity: Construct super-cells from spliced and un-spliced matrices

Description

Usage

Value

Arguments