ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling. ReDeeM is a single-cell multiomics platform featuring ultra-sensitive mitochondrial DNA (mtDNA) variant calling and joint RNA+ATAC profiling. ReDeeM enables fine-scale lineage tracing at single cell level, allowing for subclonal and phylogenetic analyses, with simultaneous integrative analyses of cell-state and gene regulatory circuits.
The analytical pipelines for ReDeeM analysis includes two parts:
- redeemV is set of in-house Bash pipeline and python scripts for mapping and deep mitochondrial mutation calling. (Input from rawdata)
- redeemR is an in-house R package for downstream lineage tracing and single cell integrative analysis. (This page, Input from redeemV)
redeemR is designed to refine the somatic mitochondiral mutations, build the single-cell phylogenetic tree and facilitate genealogical and clonal/subclonal-resolved single-cell multiomics analysis.
You can install the development version of redeemR:
devtools::install_github("chenweng1991/redeemR")
library(redeemR)- 2024-8-24 We provide an additional filtering option in the ReDeeM-R package. This approach effectively eliminates the position biases, leads to a mutational signature indistinguishable from bona fide mitochondrial mutations, and removes excess low molecule high connectedness mutations with high sensitivity. Please see Document Use filter-2 below
- Getting started
- Use filter-2
- ReDeeM paper analysis reproducibility
- Extended ReDeeM robustness analysis
Please check out our study of human hematopoiesis using ReDeeM Deciphering cell states and genealogies of human hematopoiesis
If you have any questions or suggestions, please feel free to contact us. Feedbacks are very welcome! (Chen Weng, cweng@broadinstitute.org)