This repository contains all code used in the statistical analysis of sequencing data from serial biopsies of patients with relapsed/refractory diffuse large B-cell lymphoma. All R packages used in the analysis can be installed reproducibly with renv, using any R version 4.1.*.
Sequencing files were processed outside of this repository using modules from LCR-Modules as follows:
| Sequencing Type | Output | Module(s) |
|---|---|---|
| genome, exome, LySeqST | Somatic variant calls | slms_3-1.0, vcf2maf-1.3 |
| genome | Somatic structural variants | svar_master-1.0 |
| genome | Copy number | battenberg-1.1 |
| exome | Copy number | strelka-1.0 |
| genome | Subclonal structure and phylogeny | pyclone-1.0 |
| genome, exome, LySeqST | Quality control (coverage metrics) | qc-1.0 |
| genome, exome, LySeqST | LymphGen classifications | lymphgen-1.0 |
| RNAseq | Immunoglobulin rearrangements | bam2fastq-1.2, mixcr-1.2 |