Repository of publication: Deterministic evolution and stringent selection during pre-neoplasia (Karlsson et al., 2023)

📁 Repository content

This GitHub repository contains the following folders:

└─ figures/: directory containing R and other code to reproduce figures (Fig.1-6)
|   └─ Figure_01/: directory containing code to reproduce Figure 1
|   └─ Figure_02/: directory containing code to reproduce Figure 2
|   └─ Figure_03/: directory containing code to reproduce Figure 3
|   └─ Figure_04/: directory containing code to reproduce Figure 4
|   └─ Figure_05/: directory containing code to reproduce Figure 5
|   └─ Figure_06/: directory containing code to reproduce Figure 6
└─ analysis/: directory containing code used for data analysis
|   └─ ECB_DNA_pipeline/: directory containing pipeline for ECB barcode analysis
|   └─ ECB_cDNA_pipeline/: directory containing pipeline for ECB cDNA analysis
|   └─ ECB_pipeline/: directory containing scripts to distinguish expressed cellular barcodes
|   └─ qDNAseq_sWGS_pipeline/: directory containing R script for copy number alteration using sWGS data

🔓 Processed data

Metadata and counts, as well as processed seurat objects available on Zenodo https://doi.org/10.5281/zenodo.6401895

🔐 Raw sequencing data

WGS, sWGS and scRNA-seq data will be available via dbGAP (phs003249.v1.p1) and Barcode-seq data is available via SRA (PRJNA838456).

✅ Citation

Kasper Karlsson, Moritz J. Przybilla, Eran Kotler, Aziz Khan, Hang Xu, Kremena Karagyozova, Alexandra Sockell, Wing H. Wong, Katherine Liu, Amanda Mah, Yuan-Hung Lo, Bingxin Lu, Kathleen E. Houlahan, Zhicheng Ma, Carlos J. Suarez, Chris P. Barnes, Calvin J. Kuo, Christina Curtis. Deterministic evolution and stringent selection during pre-neoplasia, Nature (2023); doi: https://doi.org/10.1101/2022.04.09.487529

✉️ Contact

For any questions, please contact Kasper Karlsson kasper.karlsson@ki.se or Moritz Przybilla mp34@sanger.ac.uk