Seurat2SCseq

This function expects a class <code>Seurat</code> object from the Seurat package as input and converts this into a RaceID <code>SCseq</code> object. The function transfers the counts, initializes <code>ndata</code> and <code>fdata</code> without further filtering, transfers the PCA cell embeddings from the <code>Seurat</code> object to <code>dimRed</code>, transfers the clustering partition, and <code>umap</code> and <code>tsne</code> dimensional reduction (if available). CAUTION: Cluster numbers in RaceID start at 1 by default. Hence, all Seurat cluster numbers are shifted by 1.

Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).

Dominic Grc3<bc>n

RaceID

Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Dominic Grün

Seurat2SCseq function

<dl><dt>Se</dt>
<dd>Seurat object.</dd>
<dt>rseed</dt>
<dd>Integer number. Random seed for sampling cluster colours.</dd></dl>

Arguments

Converting a Seurat object to a RaceID/VarID object — Seurat2SCseq

<dl>

<dt>Se</dt>
<dd>Seurat object.</dd>


<dt>rseed</dt>
<dd>Integer number. Random seed for sampling cluster colours.</dd>

</dl>

Seurat2SCseq: Converting a Seurat object to a RaceID/VarID object

Description

Usage

Value

Arguments