System requirements and Installation

All requirements may be found in requirements.txt and r_requirements.txt. All packages used are previously published; please refer to the corresponding guides for installation instructions/times. Processed data generated using lpWGS, snRNA-seq, and TCR-seq have been deposited at GEO (GSE308433, GSE308434, GSE308435).

Files creating figures:

Figure 1:

• Initial_processing/
• Annotation/
• Mel_Figures_5_6_7_S6_S7_S8.ipynb

Figure 2:

• Mel_Echidna_run.ipynb
• Mel_Figure_2.ipynb

Figure 3:

• Mel_Echidna_run.ipynb
• Mel_Figure_3_KUL.ipynb
• Mel_Figures_3_S2_S3.ipynb

Figure 4:

• Mel_Echidna_run.ipynb
• Mel_Figures_4_S4_S5_S8.ipynb

Figure 5:

• tcells/
• Mel_Figures_5_6_7_S6_S7_S8.ipynb

Figure 6:

• myeloid/
• Mel_Figures_5_6_7_S6_S7_S8.ipynb

Figure 7:

• contact_tracing/
• Mel_Figures_4_S4_S5_S8.ipynb
• Mel_Figures_5_6_7_S6_S7_S8.ipynb

Figure S1:

• patient_overview.R
• milo/

Figure S2:

• Mel_Figures_3_S2_S3.ipynb

Figure S3:

• Mel_Figures_3_S2_S3.ipynb

Figure S4:

• Mel_Figures_4_S4_S5_S9.ipynb

Figure S5:

• Mel_Figures_4_S4_S5_S9.ipynb

Figure S6:

• tcells/
• tcr/
• Mel_Figures_5_6_7_S6_S7_S8.ipynb

Figure S7:

• myeloid/
• Mel_Figures_5_6_7_S6_S7_S8.ipynb

Figure S8:

• contact_tracing/
• Mel_Figures_5_6_7_S6_S7_S8.ipynb

Figure S9:

• Mel_Figures_4_S4_S5_S9.ipynb