This repository contains the R scripts used to generate the figures for the manuscript:
A high MAPK cell state drives metastatic dissemination in colorectal cancer
Submitted to Nature Cancer
Melanie Heinlein1, Ginny X Li2, Noelyn Kljavin1, Amanda R Moore1,4, Brian Biehs1, Liming Tao3, Soufiane Boumahdi1, Farnaz Mohammadi5, Minyi Shi6, Yuxin Liang6, Hartmut Koeppen7, Nicolò Riggi3, Robert Piskol5, Frederic J de Sauvage1*
1 Department of Research Oncology, Genentech, Inc, South San Francisco, CA, USA.
2 Roche Digital Technoloty, Hoffman-La Roche Canada, Mississauga, ON, Canada.
3 Department of Cell and Tissue Genomics, Genentech, Inc, South San Francisco, CA, USA.
4 Department of Discovery Oncology, Genentech, Inc, South San Francisco, CA, USA.
5 Computational Sciences Center of Excellence, Genentech, Inc, South San Francisco, CA, USA.
6 Department of Proteomic and Genomic Technologies, Genentech, Inc, South San Francisco, CA, USA.
7 Department of Research Pathology, Genentech, Inc, South San Francisco, CA, USA.
Additional information *Corresponding author
The code is provided to ensure transparency and enable the reproduction of the plots
- R version 4.2 or higher
This project is licensed under the MIT License. See the License.txt file for details.
- 1 Clone this repository
- 2 Open the project in RStudio
- 3 Run each R markdown file in the /R folder to get results
- Included Data: this repo contains processed .rds files and text files necessary to reproduce figures in the manuscript located in the /data folder.
- Sensitivity & Value: The included data is not high-value. It is aggregated and anonymized. It does not contain any sensitive compound data or chemical structures.
- Data not included: To be explicit, this repository does not contain: Any raw sequencing data (e.g., FASTQ, BAM, or raw .h5ad files). Any AI/ML model weights. Any test code, training data, or evaluation data. Any proprietary algorithms or internal software.