markerList2mat

This function converts a list of marker genes for different cell types or clusters into a matrix, where rows represent cell types and columns represent marker genes. The matrix contains the frequency of each marker gene across the different cell types.

Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. More details on the methods related to our paper currently under submission. A full reference to the paper will be provided in future versions once the paper is published.

Xiao Zhang

CAESAR.Suite

CAESAR: a Cross-Technology and Cross-Resolution Framework for
Spatial Omics Annotation

Wei Liu

Jin Liu

markerList2mat function

<dl><dt>markerList</dt>
<dd>A list where each element contains marker genes for different cell types or clusters. Each element of the list is a named list, where the names are the cell types and the values are the marker genes for that cell type. Generally, it is a list of the output of function <code>marker.select</code>.</dd></dl>

Arguments

Convert Marker List to a Weighted Matrix — markerList2mat

<dl>

<dt>markerList</dt>
<dd>A list where each element contains marker genes for different cell types or clusters. Each element of the list is a named list, where the names are the cell types and the values are the marker genes for that cell type. Generally, it is a list of the output of function <code>marker.select</code>.</dd>

</dl>

markerList2mat: Convert Marker List to a Weighted Matrix

Description

Usage

Value

Arguments

See Also

Examples