make_seurat_annot

This function takes in raw counts (and potentially meta data) to make a Seurat object
and process it

This takes spatial single-cell-type RNA-seq data (specifically designed for Slide-seq v2) that calls copy number alterations (CNAs) using pseudo-spatial binning, clusters cellular units (e.g. beads) based on CNA profile, and visualizes spatial CNA patterns. Documentation about 'SlideCNA' is included in the the pre-print by Zhang et al. (2022, <doi:10.1101/2022.11.25.517982>). The package 'enrichR' (>= 3.0), conditionally used to annotate SlideCNA-determined clusters with gene ontology terms, can be installed at <https://github.com/wjawaid/enrichR> or with install_github("wjawaid/enrichR").

Diane Zhang

SlideCNA

Calls Copy Number Alterations from Slide-Seq Data

Johanna Klughammer

Jan Watter

Broad Institute of MIT and Harvard 

make_seurat_annot function

<dl><dt>cb</dt>
<dd>sparse counts matrix (genes x cells/beads)</dd>
<dt>md</dt>
<dd>data.frame of meta data for cells/beads if specific annotations known</dd>
<dt>seed_FindClusters</dt>
<dd>seed number for FindCLusters</dd>
<dt>seed_RunTSNE</dt>
<dd>seed number for RunTSNE</dd>
<dt>seed_RunUMAP</dt>
<dd>seed number for RunUMAP</dd></dl>

Arguments

Creation of Seurat object — make_seurat_annot

<dl>

<dt>cb</dt>
<dd>sparse counts matrix (genes x cells/beads)</dd>


<dt>md</dt>
<dd>data.frame of meta data for cells/beads if specific annotations known</dd>


<dt>seed_FindClusters</dt>
<dd>seed number for FindCLusters</dd>


<dt>seed_RunTSNE</dt>
<dd>seed number for RunTSNE</dd>


<dt>seed_RunUMAP</dt>
<dd>seed number for RunUMAP</dd>

</dl>

make_seurat_annot: Creation of Seurat object

Description

Usage

Value

Arguments