/tx100_rna_2024

tx100_rna_2024

Primary LanguageR

Tracking non-genetic evolution from primary to metastatic ccRCC: TRACERx Renal 100

Structure and content of this repository

This repository contains all the code and data necessariy to reproduce the results, figures (main and supplementary) and tables of the manuscript "Tracking non-genetic evolution from primary to metastatic ccRCC: TRACERx Renal".

Running the scripts in analysis/scripts reproduces all the analyses in the manuscript, with the exception of single-cell RNA-Seq results, for which data availability is controlled by corresponding authors. Auxiliar functions are located in src. Input, intermediate and output data are provided, so that each script is runnable without the need to run previous scripts.

We provide below an index of what scripts reproduce the different figures and tables in the manuscript.

Linking code to manuscript figures (main and supplementary) and tables

The table below explicitly lists which code reproduces each figure in the manuscript:

Figure type Figure number Code location
Main 1a analysis/scripts/umap.R
Main 1b analysis/scripts/estimate_transcriptional_ited.R
Main 1c analysis/scripts/correlates_primary_ited.R
Main 1d analysis/scripts/survival_transcriptional_ited.R
Main 2a analysis/scripts/td_prim_norm.R
Main 2b analysis/scripts/td_prim_met.R
Main 2c analysis/scripts/td_vs_clonal_dist.R
Main 2d analysis/scripts/td_metclone.R
Main 2e analysis/scripts/ssgsea_early_late.R
Main 2f None, manually using graphical design software
Main 3a None, manually using graphical design software
Main 3b analysis/scripts/paired_ssgsea_driver.R
Main 3c analysis/scripts/cgas_dea.R
Main 3d None, from mIF results
Main 3e None, from mIF results
Main 3f None, from mIF results
Main 3g analysis/scripts/cgas_surv_tx.R
Main 3h analysis/scripts/cgas_surv_tcga.R
Main 4a analysis/scripts/heatmap_tme_ith.R
Main 4b analysis/scripts/correlates_primary_tme_ith.R
Main 4c analysis/scripts/survival_tme_ith.R
Main 4d analysis/scripts/ssgsea_early_late.R
Main 4e analysis/scripts/tme_by_evotype.R
Main 5a analysis/scripts/get_tcr_bcr_sim.R
Main 5b analysis/scripts/TCR_BCR_similarity_survival.R
Main 5c analysis/scripts/tcr_bcr_matches.Rmd
Main 5d analysis/scripts/tcr_bcr_vs_clonal_dist.R
Main 5e analysis/scripts/tcr_metclone.R
Main 6a analysis/scripts/fig6_HERV_analysis.R
Main 6b analysis/scripts/fig6_HERV_analysis.R
Main 6c analysis/scripts/fig6_HERV_analysis.R
Main 6d analysis/scripts/fig6_HERV_analysis.R
Supplementary 1 analysis/scripts/generate_oncoprint.R
Supplementary 2 analysis/scripts/umap.R
Supplementary 3 analysis/scripts/lme_transcriptional_pc.R
Supplementary 4 analysis/scripts/lme_transcriptional_pc.R
Supplementary 5 analysis/scripts/umap.R
Supplementary 6 None, manually using graphical design software. Mock scatter plots generated in src/td_mock_example.R
Supplementary 7 analysis/scripts/survival_transcriptional_ited.R
Supplementary 8 analysis/scripts/prim_norm_td_clonal.R
Supplementary 9 None, manually using graphical design software
Supplementary 10 analysis/scripts/td_vs_clonal_dist.R
Supplementary 11 None, manually using graphical design software
Supplementary 12 scRNA-Seq data is not publically available, hence code is not available
Supplementary 13 analysis/scripts/surv_9p_prolif.R
Supplementary 14 None, from mIF results
Supplementary 15a analysis/scripts/cgas_surv_tx.R
Supplementary 15b analysis/scripts/cgas_surv_tcga.R
Supplementary 16 analysis/scripts/surv_pan_cancer_slc19a1.R
Supplementary 17 analysis/scripts/04_consensustme_vs_histo.R
Supplementary 18 analysis/scripts/tme_dist_vs_clonal_dist.R
Supplementary 19 analysis/scripts/TME_early_late.R
Supplementary 20 analysis/scripts/CD8_paired_drivers.R
Supplementary 21 analysis/scripts/TCR_BCR_similarity_survival.R
Supplementary 22 analysis/scripts/tcr_bcr_matches.Rmd
Supplementary 23 analysis/scripts/tcr_bcr_matches.Rmd
Supplementary 24 analysis/scripts/tcr_bcr_vs_clonal_dist.R
Supplementary 25 analysis/scripts/fig6_HERV_analysis.R
Supplementary 26 analysis/scripts/fig6_HERV_analysis.R
Supplementary Table 1 analysis/scripts/normal_prim_ssgsea.R
Supplementary Table 1 analysis/scripts/prim_met_ssgsea.R
Supplementary Table 3 data/meta/martinez_ruiz_2023_hallmark_gs_groups.txt. Obtained from Martínez-Ruiz et al, Nature 2023
Supplementary Table 4 analysis/scripts/cgas_dea.R
Supplementary Table 5 analysis/scripts/ssgsea_early_late.R