mitoClone2

mitoClone2 identifies clonal populations in single-cell RNA-sequencing data by integrating mitochondrial heteroplasmic variants discovered from BAM alignment files.

Key Features:

• Variant Identification: Identifies variants in mitochondrial genomes from BAM alignment files.
• RNA Editing Filtering: Filters variants to remove RNA editing events.
• Phylogenetic Analysis: Estimates evolutionary relationships (phylogenetic trees) of variants.
• Clonal Grouping: Groups single cells into clones based on mitochondrial variants.
• Visualization: Visualizes mutations and provides additional genomic context.
• Multiplexed BAM Input: Directly uses multiplexed BAM files as input.
• Genome Annotations: Includes annotations for both human and mouse mitochondrial genomes.
• Helper Functions: Provides helper functions for calling, filtering, clustering, and visualizing variants.
• Tool Compatibility: Built-in compatibility with commonly used tools for delineation of clonal structure.

Scientific Applications:

• Clonal Population Dynamics: Elucidates clonal structure in single-cell RNA-sequencing data using mitochondrial variants to study disease and development.
• Mitochondrial Heteroplasmy Analysis: Investigates mitochondrial genomic variability arising from high mitochondrial mutation rates under healthy and diseased conditions.

Methodology:

The package identifies variants in mitochondrial genomes from BAM alignment files, filters these variants to remove RNA editing events, estimates their evolutionary relationship (phylogenetic tree), and groups single cells into clones.