Request for Detailed Environment Dependencies to Reproduce Analysis

[moshi9000]

Hi,
Thank you for your important work on Galeano-Nino-Bullman-Intratumoral-Microbiota_2022 and for sharing the code publicly. I am attempting to reproduce the analysis locally, but unfortunately, I do not have access to the Fred Hutch computing cluster or its internal EasyBuild modules.

To overcome this limitation, would you kindly provide the ​complete list of environment dependencies used in the project? Specifically:

1.​Software Versions:
A list of all tools loaded via ml (e.g., CellRanger/6.1.1, R/4.1.2, etc.), including versions.
Critical R/Python packages (e.g., phyloseq, DESeq2, scanpy) and their versions.

2.​Environment Replication Files:
If possible, could you share any of the following?
A conda environment.yml file.
R sessionInfo() or renv.lock output.
A Dockerfile or Singularity definition file.
Even a minimal dependency list would greatly help the community replicate your work outside the Fred Hutch environment. Thank you for considering this request, and please let me know if you need further clarification!

Best regards,Moshi