Accurate circadian time prediction from a single bulk and single-cell transcriptomic data by tauFisher

As the circadian clock regulates fundamental biological processes, disrupted clocks are often observed in patients and diseased tissues. Determining the circadian time of the patient or the tissue of focus is essential in circadian medicine and research. Here we present tauFisher, a computational pipeline that accurately predicts circadian time from a single transcriptomic sample. We demonstrate tauFisher’s outstanding performance in both bulk and single cell transcriptomic data collected from multiple tissue types and experimental settings. Application of tauFisher at a cell-type level in a single cell RNA-seq dataset collected from mouse dermal skin implies that greater circadian phase heterogeneity may explain the dampened rhythm of collective core clock gene expression in dermal immune cells compared to dermal fibroblasts. Given its robustness and generalizability across assay platforms, experimental setups, and tissue types, as well as its potential application in single cell RNA-seq data analysis, tauFisher is a promising tool that facilitates circadian medicine and research. Dermal cells were collected from WT C57BL/6J mouse dorsal skin every four hours for three days under the 12:12 light-dark cycle. The Chromium Single Cell 3' v3 (10x Genomics) libraries were prepared and sequenced with Illumina NovaSeq6000.