Millefy

Millefy visualizes read coverage across individual cells and integrates these profiles with genomic context to reveal locus-specific transcriptional heterogeneity.

Key Features:

• Read Coverage Visualization: Displays read coverage for all individual cells simultaneously as heat maps to reveal variation in transcriptional activity and RNA processing.
• Dynamic Reordering of Cells: Uses diffusion maps to reorder cells by locus-specific pseudotime, highlighting local region-specific heterogeneity in read coverage.
• Genomic Context Integration: Embeds per-cell read coverage within genomic context to relate spatial genomic features to RNA transcription and processing.

Scientific Applications:

• Mouse embryonic stem cells: Applied to mouse embryonic stem cells to reveal variability in transcribed regions such as antisense RNAs, 3' untranslated region (UTR) lengths, and enhancer RNA transcription.
• Triple-negative breast cancers: Applied to triple-negative breast cancers to investigate cellular heterogeneity and complex gene regulatory mechanisms via region-specific read coverage patterns.

Methodology:

Millefy leverages diffusion maps to reorder cells based on locus-specific pseudotime and visualizes per-cell read coverage as heat maps embedded in genomic context.