Chih-Yuan Hsu is first author of all-department paper in Bioinformatics
Congratulations to research assistant professor Chih-Yuan Hsu (first author) and professors Qi Liu and Yu Shyr (corresponding authors) on the publication of A distribution-free and analytic method for power and sample size calculation in single-cell differential expression in Bioinformatics. The paper addresses potential deviations from true data distribution in power and sample size calculation by offering a new method, scPS, that "stands out by making no assumptions about the data distribution and considering cell-cell correlations within individual samples. scPS is a rapid and powerful approach for designing experiments in single-cell differential expression analysis." There are web versions of scPS's independent two-group comparison and paired-group comparison tools as well.
An illustration of sample sizes and cells per sample in aiming toward a power of .80. This is Figure 1.2-1 in the independent file set for the scPS package on GitHub.
First-authored paper in Genome Biology by Jia Li
Congratulations to postdoctoral fellow Jia Li on the publication of "aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph" in Genome Biology on August 1, with professors Yu Shyr and Qi Liu as corresponding authors. The paper offers a new method "to simultaneously identify abundant and rare cell types based on an adaptive k-nearest neighbor graph with optimization," doing so "more accurately than general and specialized methods." {aKKNO} and related tutorials are free and available on GitHub and Zenodo.
Figure 1 in the paper provides an overview of how aKNNO works.