Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants

• DOI: 10.1093/nargab/lqae095
• Publication Date: 2024-08-09T18:14:12Z
• Authors: Benjamin Story; Lars Velten; Gregor Mönke; Ahrmad Annan; Lars Steinmetz
• Keywords: 0301 basic medicine; 03 medical and health sciences; Computational Methods for Transcriptome Analysis

Clonal cell population dynamics play a critical role in both disease and development. Due to high mitochondrial mutation rates under healthy diseased conditions, genomic variability is particularly useful resource facilitating the identification of clonal structure. Here we present mitoClone2, an all-inclusive R package allowing for populations through integration heteroplasmic variants discovered from single-cell sequencing experiments. Our streamlines investigation this phenomenon by providing: built-in compatibility with commonly used tools delineation structure, ability directly use multiplexed BAM files as input, annotations human mouse genomes, helper functions calling, filtering, clustering, visualizing variants.