R scripts and resources to accompany Tang/Fewings et al 2020 manuscript
| File | Description |
|---|---|
| S01_tSNE.Rmd | Performs t-Distributed Stochastic Neighbor Embedding on clones to determine relatedness and confirm different cell tyoes |
| S02_RNA_DE_celltype.Rmd | Analyses RNA to identify genes significantly differentially expressed in different cell types, thereby confirming cell morphology |
| S03_MB_Signature_analysis.Rmd | Plots mutation burdens of clones and identifies the proportion of their mutations associated with previously defined mutation signatures |
| S04_RNA_MB_DE.Rmd | Identifies significantly differentially expressed genes associated with changes in mutation burden within one anatomic site |
| S05_RNA_sexchrom_dels.Rmd | Calculates coverage over sex chromosomes and creates t-SNE plot to identify clones with sex chromosome deletion |
| File | Description | Used in script |
|---|---|---|
| Ensembl_IDs.txt | List of Ensembl transcript IDs and associated gene names | S01, S02, S04, S05 |
| ensemblIDS_chromosomes.txt | List of Ensembl transcript IDs, associated gene names, and the chromosome in which they reside | S05 |
| exome_mutation_list_csq_UV_MAF_20200211.txt | Combined list of all validated or inferred mutations identified in exome data | S03 |
| mutation_burdens_20200211.csv | Calculated mutation burdens for each clone | S03 |
| mutation_burdens_plot_20200211.csv | Calculated mutation burdens for each clone reorganised in script S03 | S04 |
| Signature7abc_PJ.csv | Mutation signatures as defined my Petljak et al 2019 | S03 |
| ucsf_mutation_list_csq_UV_MAF_20200211.txt | Combined list of all validated or inferred mutations identified in UCSF500 data | S03 |
Direct output of RSEM gene quantification analysis. An output for each clone is in the RNA/ directory