anndata_2_supercell

Convert Anndata metacell object (Metacell-2 or SEACells) to Super-cell like object

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

anndata_2_supercell function

<dl><dt>adata</dt>
<dd>anndata object of metacells
(for example, the output of <a href="https://metacells.readthedocs.io/en/latest/_modules/metacells/pipeline/collect.html#collect_metacells"><code>collect_metacells()</code></a> for Metacells
or the output of <a href="https://github.com/dpeerlab/SEACells/blob/406ebd3a7ee200788358464b345fa0c8d88fda69/SEACells/core.py#L532"><code>SEACells.core.summarize_by_SEACell</code></a>)
Please, **make sure**, adata has `uns['sc.obs']` field containing observation information of single-cell data, in particular,
a column 'membership' (single-cell assignemnt to metacells)</dd>
<dt>simplification.algo</dt>
<dd>metacell construction algorithm (i.e., Metacell2 or SEACells)</dd></dl>

Arguments

Convert Anndata metacell object (Metacell-2 or SEACells) to Super-cell like object — anndata_2_supercell

<dl>

<dt>adata</dt>
<dd>anndata object of metacells
(for example, the output of <a href='https://metacells.readthedocs.io/en/latest/_modules/metacells/pipeline/collect.html#collect_metacells'><code>collect_metacells()</code></a> for Metacells
or the output of <a href='https://github.com/dpeerlab/SEACells/blob/406ebd3a7ee200788358464b345fa0c8d88fda69/SEACells/core.py#L532'><code>SEACells.core.summarize_by_SEACell</code></a>)
Please, **make sure**, adata has `uns['sc.obs']` field containing observation information of single-cell data, in particular,
a column 'membership' (single-cell assignemnt to metacells)</dd>


<dt>simplification.algo</dt>
<dd>metacell construction algorithm (i.e., Metacell2 or SEACells)</dd>

</dl>

anndata_2_supercell: Convert Anndata metacell object (Metacell-2 or SEACells) to Super-cell like object

Description

Usage

Value

Arguments