These are supporting scripts for our manuscript titled: Predicted meta-omics: a potential solution to multi-omics data scarcity in microbiome studies.
The data used for the main experiments was downloaded from the Inflammatory Bowel Disease Multi'omics Database:
- IBDMDB: metagenomics (genes, taxa, and pathways), metatranscriptomics, metaproteomics and metabolomics.
The datasets used for the "reproducibility" experiments were downloaded from two sources:
- Gut microbiome dataset published by Franzosa et al. [1]
- The Curated Gut Microbiome Metabolome Data Resource: specifically one ESRD [2] and one colorectal cancer [3] dataset
[1] Franzosa, Eric A., et al. "Gut microbiome structure and metabolic activity in inflammatory bowel disease." Nature microbiology 4.2 (2019): 293-305.
[2] Wang, Xifan, et al. "Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents." Gut 69.12 (2020): 2131-2142.
[3] Yachida, Shinichi, et al. "Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer." Nature medicine 25.6 (2019): 968-976.