Oscope

Oscope identifies oscillatory gene expression patterns in single-cell RNA sequencing (scRNA-seq) data from unsynchronized cell populations to characterize temporal transcriptional dynamics.

Key Features:

• Sine Model Module: Fits sine-wave models to expression data to search for candidate pairs of oscillating genes.
• K-medoids Clustering Module: Clusters candidate oscillator pairs into groups using k-medoids to group similar expression profiles.
• Extended Nearest Insertion Module: Reconstructs the base cycle order for each group of oscillators to determine sequences of expression peaks and troughs.
• Base Cycle Profile Detection: Discerns base cycle profiles of oscillating genes across cells to define cyclical expression patterns.
• Noise and Artifact Robustness: Uses clustering and model fitting approaches intended to handle noise and technical variability in scRNA-seq data.
• Platform-specific Artifact Identification: Detects potential artifacts associated with platforms such as the Fluidigm C1 system.

Scientific Applications:

• Developmental biology: Identifies oscillatory transcriptional programs relevant to developmental processes from unsynchronized scRNA-seq data.
• Circadian rhythm studies: Detects genes exhibiting cyclical expression consistent with circadian or other periodic regulatory processes.
• Temporal regulation characterization: Characterizes the timing and ordering of gene expression peaks and troughs to study temporal regulation.
• Platform artifact assessment: Assesses and helps identify platform-specific technical artifacts, exemplified by Fluidigm C1, that may confound oscillation detection.

Methodology:

Oscope fits sine-wave models to identify candidate oscillating gene pairs, clusters candidate pairs using k-medoids, and reconstructs base cycle order for each cluster using an extended nearest insertion procedure.