README.md

Tracking rare single donor and recipient immune and leukemia cells after allogeneic hematopoietic cell transplantation using mitochondrial DNA mutations

Code to reproduce analyses of Penter et al., Blood Cancer Discovery 2024.

intermediate files

The data needed to reproduce the analyses is hosted on OSF. They need to be downloaded and used to populate the data/ folder.

Part1, Part2, Part3, Part4, Part5, Part6

Main figures

The code for the panels of the main figures can be found here. See individual subdirectories for further indications.

Figure 1 | figure_CLL_WES_RNA
Figure 2 | figure_CLL_WES_RNA, figure_coevolution
Figure 3 | figure_mixing
Figure 4 | figure_IST
Figure 5 | figure_10026
Figure 6 | figure_AML_coevolution
Figure 7 | figure_AML_coevolution

Supplementary figures

The code for the panels of the supplementary figures can be found here. See individual subdirectories for further indications.

Suppl. Fig. 1 | figure_CLL_WES_RNA
Suppl. Fig. 2 | figure_CLL_WES_RNA
Suppl. Fig. 3 | figure_CLL_WES_RNA
Suppl. Fig. 4 | figure_CLL_WES_RNA
Suppl. Fig. 5 | figure_CLL_WES_RNA
Suppl. Fig. 6 | figure_CLL_WES_RNA
Suppl. Fig. 7 | figure_coevolution
Suppl. Fig. 8 | figure_coevolution
Suppl. Fig. 9 | figure_coevolution
Suppl. Fig. 10 | figure_mixing
Suppl. Fig. 11 | figure_mixing
Suppl. Fig. 12 | figure_mixing
Suppl. Fig. 13 | figure_IST
Suppl. Fig. 14 | figure_IST
Suppl. Fig. 15 | figure_IST
Suppl. Fig. 16 | figure_10026
Suppl. Fig. 17 | figure_10026
Suppl. Fig. 18 | figure_AML_coevolution
Suppl. Fig. 19 | figure_AML_coevolution
Suppl. Fig. 20 | figure_AML_coevolution