Story, Benjamin A.Velten, LarsMönke, GregorAnnan, AhrmadSteinmetz, Lars M.2024-12-022024-12-022024Story B, Velten L, Mönke G, Annan A, Steinmetz L. Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants. NAR Genom Bioinform. 2024 Aug 9;6(3):lqae095. DOI: 10.1093/nargab/lqae0952631-9268http://hdl.handle.net/10230/68869Clonal cell population dynamics play a critical role in both disease and development. Due to high mitochondrial mutation rates under both healthy and diseased conditions, mitochondrial genomic variability is a particularly useful resource in facilitating the identification of clonal population structure. Here we present mitoClone2, an all-inclusive R package allowing for the identification of clonal populations through integration of mitochondrial heteroplasmic variants discovered from single-cell sequencing experiments. Our package streamlines the investigation of this phenomenon by providing: built-in compatibility with commonly used tools for the delineation of clonal structure, the ability to directly use multiplexed BAM files as input, annotations for both human and mouse mitochondrial genomes, and helper functions for calling, filtering, clustering, and visualizing variants.application/pdfeng© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.RNAADN mitocondrialinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/nargab/lqae095info:eu-repo/semantics/openAccess