peco

peco predicts continuous cell cycle progression using single-cell RNA sequencing (scRNA-seq) data to identify cyclic trends of gene expression levels along the cell cycle.

Key Features:

• Continuous phase assignment: Assigns continuous cell cycle phase rather than discrete cell cycle stages using scRNA-seq data.
• Training data included: Provides scRNA-seq data from 6 individual induced pluripotent stem cell (iPSC) lines paired with continuous cell cycle phase derived from FUCCI fluorescence imaging data.
• Cyclic trend identification: Enables detection of cyclic patterns in gene expression levels as a function of cell cycle progression.

Scientific Applications:

• Cell cycle analysis: Assigns precise continuous cell cycle phase to individual cells in scRNA-seq datasets.
• Gene expression dynamics: Identifies and characterizes periodic gene expression patterns throughout the cell cycle.
• iPSC research: Supports studies using induced pluripotent stem cells by providing validated training data and methods.

Methodology:

Supervised approach using scRNA-seq data integrated with FUCCI fluorescence imaging-derived continuous cell cycle phase annotations from 6 individual iPSC cell lines.