Fig. 6: Benchmarking analysis shows that DOLPHIN produces superior cell embeddings, demonstrated by improved cell clustering accuracy.
From: DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads
This benchmarking analysis highlights the superior cell embeddings generated by DOLPHIN, achieved through the integration of exon-level quantification and junction reads. Better cell clustering accuracy demonstrates the improved quality of these embeddings, evaluated using Adjusted Rand Index (ARI), Normalized Mutual Information (NMI), Completeness Score (CS), Adjusted Mutual Information (AMI), and Fowlkes–Mallows Index (FMI) across full-length PBMC (a), 10X colon (b), and 10X rectum datasets (c). Each score is based on N = 100 bootstrapping replicates using different random seeds (technical replicates). Boxes indicate the interquartile range (IQR, 25th to 75th percentile), with the line inside each box representing the median. Whiskers extend to the most extreme data points within 1.5 times the IQR from the quartiles. P values from one-sided Student’s t-tests: *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001; n.s. not significant. Exact P values are provided in the source data. Source data are provided as a Source Data file.
