Manual annotation of cell types in single cell RNA-seq
I have recently started working with scRNA-seq data. I am following the tutorials by the creators of Seurat. In the final section titled “Assigning cell type identity to clusters”, the authors mention that
Fortunately in the case of this dataset, we can use canonical markers
to easily match the unbiased clustering to known cell types:
After this, they define a set of genes and the corresponding cell types and use that to annotate their dataset. I wanted to apply the same concept to a different scRNA-seq based breast cancer dataset. I derived the final list of clusters but got stuck while trying to manually annotate them. Basically, I have downloaded a list of markers (a matrix containing genes and cell types) from the Cell Marker database. I also have an expression matrix with rows as genes and columns as cells. Now how do I manually assign each cell to a particular cell type?
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