Please read Dr. Ghaddar’s article in Bioinformatics titled, “Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census.“
Single cell RNA-seq (scRNA-seq) has enabled annotation and transcriptional characterization of cell-types in multicellular species. Cell-type annotation is a critical and often difficult and time-consuming first step in any scRNA-seq data analysis. Typical annotation pipelines involve cell clustering followed by comparison of cluster differentially expressed genes with cell-type marker genes databases. While this approach is suitable for major, well-defined cell-types, it can be challenging to annotate cells from noisy datasets or to identify cell-subtypes for which marker genes are overlapping, poorly expressed, or incompletely described. This problem is especially pertinent while analyzing scRNA-seq data from perturbation experiments, disease contexts such as cancer, or treatment conditions. To read the full article.
Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census. Ghaddar B, De S. 2023 Dec 1;39(12):btad714. PMID: 38011649 PMCID: PMC10713118 DOI: 10.1093/bioinformatics/btad714