DOI: 10.5281/zenodo.16886808
title: RMD files, associated RDS files and datasets,  FISH metadata and Biorender license related to NMED-A140141

description: Dear Editor and Reviewer,

First of all, thank you for taking the time to review this work. To make your exploration of the code as smooth and efficient as possible, we have prepared a detailed mapping between the Supplementary Tables and the corresponding analysis scripts. You will find this information in the attached Excel file ("Tables_assigned_codes").

Overview of the code and its purpose : 

Below is a brief description of each script, including its purpose and instructions for running it:

1/ Cohort_description_MTB : Provides an overview of sample and cohort counts before and after filtering : 





Load the "clinical_data_phyloseq" file provided in version V2, together with the following objects: "physeq", "physeq_glom13", "merged_phy", "remove_control_final", and "remove_oct_final". 




Then, execute the script step by step (chunk by chunk) in the order provided. 




This code corresponds to the generation of the following tables and figures : Figure 1 and 2.d, Supplementary Tables S1, S2, S3, S13, S14, S15, S16, S31, S32. 



2/ Decontamination_pipeline : Contains all the steps related to data filtration, from the raw data to the final phyloseq object.

3/ Alluvial_plot_tables : Includes all details and data related to each step of the decontamination pipeline. It contains counts at both the phylum and genus levels, before and after filtering, as well as the alluvial plots illustrating these changes.

4/ Prevalence_occurrence_predominance : Describes the distribution of taxa across different sample types and cohorts. It also includes the predominance score attribution, species and ASV-level assignments, and the Fusobacterium nucleatum animalis Clade 2 classification.

5/ Tumor_versus_NAT : Performs volcano plot comparisons of taxa significantly abundant between tumor and NAT in CRC primary tumors (PT) and metastases (MT), adjusted per patient.

6/ taxa_sharing : Identifies shared taxa at the genus and ASV levels between CRC PT and MT within individual patients.

7/ figures_METBIOME : Provides direct access to the final improved figures presented in the paper, without needing to go through the full scripts. All previous figure versions are still accessible in the corresponding scripts, along with the Supplementary Tables and Figures.

Additional Files Provided : 

To facilitate the reproducibility of the results, we have included:

- All necessary files to run the code, including RDS files and datasets.

- Biorender license information for the custom-made figures included in the paper.

- FISH data : Including the files, metadata, and images for each image presented in the main article.

Additionally, if you feel that the clarity or flow of the code could be improved in any way, please do not hesitate to ask. We are more than happy to refine or adjust it upon request to ensure smooth readability and usability.

If you have any questions or need further clarifications, please don’t hesitate to reach out. We truly appreciate your time and efforts in reviewing this work!

Best regards,Philippe Stevens, on behalf of the co-authors